Computational Structural Biology Lab

Bound^a

RNA length (nt)

Binding Affinity (Kd) (M)^g

Temperature (K)^h

pHⁱ

ΔG
(kcal/mol) ^j

Exp
Technique^k

BSA (Ų)^b

RMSD Å

Category^f

PubMed ID^(l)

PDB ID

Protein

RNA

Cα-rmsd^c

P-rmsd^d

i-rmsd^e

Crystal

Solution

Cα

P

I. Unbound-Unbound cases (17)

(A) Complexes with tRNA (7)

1ASY (A:R)

‎S. cerevisiae aspartyl-tRNA synthetase

tRNA-Asp

75

76

3.0x10^-8

310

5.5

-10.66

FBA

4430

1.5

4.9

1.3

3.3

R

10452887

1QTQ (A:B)

E. coli glutaminyl-tRNA synthetase

tRNA-Gln

75

76

3.6x10^-7

310

5.2

-9.13

Binding kinetics

5202

1.6

4.8

1.8

6.4

S

15845537

2DRB (A:B)

A. fulgidus CCA-adding enzyme

tRNAminiCCA

35

73

6.7x10^-8

298

8.5

-9.78

EMSA

3198

1.1

3.4

1.8

4.2

S

14592988

2FMT (A:C)

E. coli methionyl-tRNAfmet transformylase

tRNAfmet

77

77

1.36x10^-7

310

7.6

-9.73

FBA

2940

1.2

2.3

0.9

2.5

R

10089442

3HL2 (AA'BB':E)

H. sapiens selenium transferase

tRNA-Sec

90

90

1.34x10^-7

300

8.0

-9.43

MST

2186

0.6

5.2

1.3

6

R

36929010

5X6B (IJEF:P)

M. jannaschii SepCysE-SepCysS

tRNA-Cys

75

75

3.5x10^-7

333

8.0

-9.84

ITC

4240

0.6

3.2

1.2

6.4

R

29142195

6LVR (C:D)

A. thaliana PRORP1

yeast tRNA-Phe

76

76

3.9x10^-7

298

7.8

-8.74

EMSA

1055

3.4

1.3

4.4

1.1

F

36753552

(B) Ribosomal proteins (3)

1DFU (P:MN)

E. coli ribosomal protein L25

5s rRNA

19

120

6.7x10^-8

298

7.6

-9.78

FBA

1690

3

5.3

3

4.4

F

365228

1MMS (A:C)

T. maritimaribosomal protein L11

23S rRNA fragment

58

60

1.20x10^-7

298

7.5

-9.44

TSR

2455

3.5

1.6

4.1

1.6

F

12954336

3IEV (A:D)

A. aeolicus GTPase era

16S rRNA

12

37

1.26x10^-8

298

7.5

-6.46

ITC

2273

0.5

7.6

0.5

8.4

R

21646538

(C) Duplex RNA (5)

1OOA (A:C)

M. musculus NF-kappaB p50

aptamer RNA

29

29

5.4x10^-9

298

7.5

-11.27

FBA

1909

6.2

6.7

5.5

7

F

12886018

2R8S (LH:R)

M. musculus synthetic FAB

ribozyme

159

159

5.1x10^-8

298

7.5

-9.94

FBA

2510

1.6

4.3

2.9

2.1

S

18162543

3SNP (A:C)

O. cuniculus iron regulatory protein 1

ferritin H IRE RNA

30

30

4.5x10^-11

298

7.5

-14.1

FBA

2872

0.7

3.8

14.5

3.3

F

17185597

2OZB (AB:C)

H. sapiens Ribonucleoprotein

U4snRNA

33

32

8.0x10^-6

277

8.0

-6.46

EMSA

2569

1.9

11

1.9

13

S

21784869

7P0V (A:B)

H. sapiens SF3A1 ubiquitin-like domain

U1 snRNA SL-4

24

24

3.32x10^-7

338

8.0

-10.02

SPR

1210

1.5

1.1

1.7

0.9

S

35101980

(D) Single-stranded RNA (2)

1JBS (A:C)

A. restrictus restrictocin

SRD RNA analogue

29

29

1.0x10^-6

298

7.2

-8.18

Fluorescence titration

1310

0.7

3.4

0.6

3.2

R

11685244

1WSU (A:E)

M. thermoacetica elongation factor SelB

SECIS RNA

23

23

1.0x10^-6

277

5.4

-7.6

EMSA

940

0.7

4.2

0.5

1.1

R

15665870

II. Unbound-Bound (83)

(A) Complexes with tRNA (5)

1U0B (B:A)

E. coli cysteinyl-tRNA synthetase

tRNA-Cys

74

74

2.70x10^-7

300

7.5

-9.02

Fluorescence titration

4560

0.7

1.0

R

15489861

3ADB (A:C)

M. jannaschii O-phosphoseryl-tRNA kinase

tRNA-Sec

92

92

4.8x10^-8

338

7.5

-11.31

EMSA

3099

22.4

27.3

F

20705242

4YVJ (AB:C)

H. influenzae tRNA methyltransferase D

tRNA

74

74

2.80x10^-7

300

8.0

-9.0

Fluorescence titration

2313

0.7

1.3

R

26183229

5B63 (A:B)

E.coli arginyl-tRNA synthetase

tRNA-Arg

77

77

2.20x10^-7

294

7.4

-8.96

Fluorescence titration

3360

1.2

1.5

S

29678554

7E8O (AB:X)

P. bacterium PRORP

pre-tRNA-His

85

85

4.30x10^-6

277

8.0

-6.8

EMSA

801

1.8

1

R

35484139

(B) Ribosomal proteins (2)

1SDS (C:FF')

M. jannaschii 50S ribosomal protein L7Ae

box H/ACA sRNA

15

84

7.5x10^-8

277

7.4

-9.03

EMSA

1200

0.3

0.4

R

12560482

5WTY (A:C)

S. cerevisiae nucleolar protein 9

18s rRNA

18

18

2.0x10^-7

300

7.9

-9.2

EMSA

3205

2.5

2.6

S

28053123

(C) Duplex RNA (26)

1YVP (B:EFH)

X. laevis Ro autoantigen

Y RNA

10

97

5.2x10^-9

277

7.5

-10.49

EMSA

4207

1.4

1.3

R

15907467

2AZ0 (AB:CD)

Flock house virus B2

siRNA

18

19

1.4x10^-9

277

7.5

-11.22

EMSA

2264

1.3

1

R

16228003

2QUX (AB:C)

Pseudomonas phage PP7 coat protein

hairpin RNA

25

27

1.26x10^-9

295

7.5

-12.01

EMSA

1754

0.9

0.5

R

18066080

2Y8W (A:B)

T. thermophilus endoribonuclease Cse3

hairpin RNA

20

20

3.6x10^-9

338

7.5

-13.05

EMSA

3258

1.1

3.1

F

21572442

2ZKO (AB:CD)

NS1 protein of influenza A

A-form dsRNA

21

21

1.2x10^-6

298

7.4

-8.07

ITC

2466

0.6

0.8

R

18813227

3A6P (AC:DE)

H. sapiens exp-5: Ran GTP

pre-microRNA

24

30

6.5x10^-9

300

7.6

-9.87

EMSA

4223

1.2

1.4

R

21947008

3DD2 (H:B)

H. sapiens thrombin

26-mer RNA

26

40

5.4x10^-10

310

7.4

-13.14

FBA

1822

0.6

0.5

R

11735341

3EQT (AB:CD)

H. sapiens helicase DHX58

dsRNA

8

20

1.05x10^-7

298

8.0

-9.51

Fluorescence titration

2705

1.2

1.2

R

19278996

3KS8 (AB:EF)

R. ebolavirus polymerase cofactor VP35

dsRNA

18

18

8.9x10^-7

300

7.5

-8.31

Dot blot

1663

0.6

0.4

R

20018665

3MOJ (B:A)

B. subtilis helicase dbpA

E.coli 23S rRNA fragment

74

74

5.4x10^-11

273

7.5

-12.82

EMSA

1758

1.0

1.0

R

20673833

3O3I (X:A)

H. sapiens Hiwi1 PAZ domain

piRNA

14

14

1.66x10^-5

298

8.0

-6.52

ITC

923

2.1

2.7

S

21193640

3RW6 (A:H)

H. sapiens nuclear RNA export factor 1

CTE RNA

62

62

9.0x10^-8

298

7.5

-9.6

ITC

2699

13.5

19

F

21822283

4ERD (AB:CD)

T. thermophila p65 C-terminal domain

stem IV of telomerase RNA

22

22

1.01x10^-7

298

7.0

-9.53

ITC

3280

1.5

1.2

R

22705372

4ZT0 (A:B)

S. pyogenes CRISPR-associated endonuclease Cas9

single-guide RNA

85

20

6.8x10^-10

300

7.5

-12.58

FBA

10845

29.6

22

F

26113724

5F5H (A:C)

M. musculus Roquin-1

Ox40 3'-UTR

22

22

8.10x10^-8

283

7.4

-9.18

SPR

1618

0.5

0.6

R

27010430

5WTK (A:B)

L. shahii CRISPR-associated endoribonuclease C2c2

crRNA

58

170

4.60x10^-8

277

7.5

-9.3

EMSA

8811

4.9

4.0

F

27256883

5ZQ8 (A:D)

S. pneumoniae RlmCD

23S rRNA U747 stemloop

12

12

5.0x10^-7

310

8.0

-8.94

EMSA

1992

1.5

1.2

R

30388185

6D12 (B:C)

H. sapiens xRRM domain of human Larp7

7SK stem-loop 4 RNA

38

25

1.29x10^-7

295

7.0

-9.30

ITC

1428

2.1

1.6

S

29946027

6DCB (A:B)

H. sapiens methylphosphate capping enzyme

5' end of 7SK RNA

36

36

1.0x10^-7

298

7.5

-9.55

ITC

697

0.7

0.3

R

30559425

6FQ3 (A:B)

D. rerio E3 ubiquitin-protein ligase TRIM71

lin-29A 5'UTR

13

13

1.57x10^-6

300

8.0

-7.78

FP

986

7.9

2

S

29674686

6SY4 (AB:C)

E. coli TetR

TetR-binding aptamer K1

43

43

5.60x10^-9

298

7.4

-11.25

ITC

1702

1.7

2

S

32052019

6PZQ (AB:IJ)

HRSV matrix M2-1

Gene-End RNA

7

7

8.67x10^-7

300

7.4

-8.32

MST

668

0.9

0.5

R

32697936

6ZDP (A:B)

C. tropicalis telomerase reverse transcriptase (724)

TWJ fragment of telomeric RNA

72

72

2.70x10^-8

293

7.8

-10.15

ITC

2629

4.1

8.4

F

33856462

7KKV (A:B)

A. halodurans OapB protein

OLE RNA target

60

100

7.0x10^-10

277

7.5

-11.6

EMSA

1365

0.7

0.7

R

32376692

7OG0 (A:EE')

H. influenzae SapA

dsRNA

17

17

4.4x10^-6

298

8.0

-7.3

ITC

597

3

2.1

S

34653190

7ZLQ (A:DE)

H. Sapiens ADAR1-dsRBD3

dsRNA

13

24

1.25x10^-7

298

7.0

-9.41

ITC

784

1.3

0.6

R

BioRxiv

(D) Single-stranded RNA (50)

1C9S (L:W1-7)

G. stearothermophilus TRAP

ssRNA

55

55

5.0x10^-10

328

8.0

-13.96

FBA

1027

0.3

0.2

R

10499579

1CVJ (A:M)

H. sapiens poly(A)-binding protein

polyA

11

25

6.70x10^-10

277

7.4

-11.63

EMSA

2822

2.7

3.9

F

14717712

1K8W (A:B)

E. coli pseudouridine synthase B

T stem-loop RNA

22

22

7.0x10^-7

300

7.5

-8.45

Fluorescence titration

2973

1.9

1.3

R

24371284

1KQ2 (ABHIKM:R)

S. aureus Hfq

7-mer RNA

7

7

5.6x10^-8

298

7.5

-9.88

Fluorescence titration

3026

0.6

0.5

R

12093755

1M8W (A:CE)

H. sapiens pumilio-homology domain

Nre1-19 RNA

16

34

6.0x10^-11

300

7.4

-14.03

EMSA

2110

0.8

0.7

R

12202039

1WPU (A:C)

B. subtilis HutP antitermination protein

hut mRNA

7

21

5.40x10^-8

300

7.5

-9.98

FBA

1360

0.2

0.2

R

15758992

2A8V (B:E)

E. coli RHO

Cytosine rich RNA

6.0

10

5.0x10^-6

298

8.0

-7.22

FBA

720

1

1.6

S

8632473

2ASB (A:B)

M. tuberculosis Nus A antiterminator

BoxC rRNA

11

13

1.15x10^-7

291

7.8

-9.23

ITC

2320

1.1

0.8

R

16193062

2IX1 (A:B)

E. coli RNase II

polyA

13

25

5.3x10^-9

277

8.0

-10.48

SPR

4160

1.6

0.9

R

18337246

2JEA (AB:C)

S. solfataricus exosome

substrate RNA

35

7.0

1.1x10^-6

293

7.5

-7.98

ITC

1533

0.3

0.3

R

17159918

2XGJ (A:C)

S. cerevisiae Mtr4

polyA

5

21

2.80x10^-6

303

6.5

-7.7

Fluorescence titration

1389

4.1

3.1

F

25414331

2XNR (A:C)

S. cerevisiae Nab3-RRM

UCUU recognition sequence

12

12

1.1x10^-4

298

7.3

-5.39

Fluorescence titration

926

1.0

1.2

R

20805243

2XZO (A:D)

H. sapiens Upf1 helicase

polyU

7

15

2.02x10^-7

293

7.5

-8.97

Fluorescence titration

2006

6.2

5.0

F

21419344

3AEV (B:C)

P. horikoshii Dim2p

P. horikoshii 16S rRNA fragment

11

11

9.8x10^-10

298

8.5

-12.28

SPR

2416

0.7

0.5

R

20363226

3BX2 (A:C)

S. cerevisiae PUF4

3' UTR binding sequence

9

9

1.36x10^-8

277

7.5

-9.96

EMSA

2467

0.6

0.5

R

18327269

3D2S (A:E)

H. sapiens MBNL1 ZnF3/4

pre-mRNA

6

18

4.0x10^-8

293

7.2

-9.91

Fluorescence titration

569

0.8

0.6

R

19043415

3MDG (AB:C)

H. sapiens CFI(m)25

pre-mRNA

6

21

6.45x10^-7

303

8.0

-8.58

EMSA

1069

0.5

0.9

R

20479262

3NMR (A:B)

H. sapiens CUG-binding protein 1

UGU-rich mRNA

12

12

6.5x10^-7

298

7.0

-8.43

ITC

1096

2.7

2.2

S

20947024

3O8C (A:C)

HCV NS3 helicase

polyU

6

18

8.7x10^-7

298

7.5

-8.26

EMSA

1909

1

1.1

R

12162749

3PF4 (B:R)

B. subtilis CspB

ssRNA

7

7

1.59x10^-7

288

7.0

-8.95

Fluorescence titration

963

0.5

0.4

R

22128343

4H5P (AB:E)

Rift valley fever virus nucleocapsid

polyU

14

25

9.6x10^-8

298

7.8

-9.56

Fluorescence titration

4482

0.9

2.1

S

23129612

4M59 (AB:CD)

Z. mays chloroplast ppr10

psaJ RNA

18

18

1.02x10^-7

295

7.5

-9.44

EMSA

7842

10.5

7.1

F

24162847

4MDX (AB:C)

B. subtilis mRNA interferase MazF

mRNA

9

9

6.40x10^-8

293

8.0

-9.64

ITC

2127

0.7

1.6

S

24120662

5DET (AB:PQ)

H. sapiens RBPMS

CAC containing ssRNA

5

17

9.0x10^-7

293

7.5

-8.11

ITC

2137

1.2

1.6

S

26347403

5EIM (A:C)

S. pombe YTH domain of spMmi1

synthetic RNA

8

8

1.10x10^-6

298

7.5

-8.12

ITC

1529

0.6

1.3

R

28735863

5ELS (AC:HI)

H. sapiens KH domain of T-STAR

synthetic RNA

6

5

3.70x10^-5

300

7.0

-6.08

FP

2313

1.5

2.9

S

26758068

5EX7 (A:B)

D. melanogaster Brat NHL domain

hunchback mRNA

8

100

1.37x10^-7

293

8.0

-9.2

MST

1639

0.4

0.6

R

24696456

5GXH (A:B)

H. sapiens Gemin5

Pre-snRNAs

8

8

2.40x10^-6

298

7.5

-7.66

ITC

1711

0.4

0.2

R

27881600

5LTA (A:E)

T. thermophila DEAH-box heicase Prp43

Synthetic RNA

16

16

4.98x10^-6

298

7.5

-7.23

Fluorescence titration

2287

2.4

2.2

S

28092261

5SZE (A:C)

A. aeolicus Hfq-RNA

PolyU

6

6

2.13x10^-8

298

8.0

-10.46

FP

502

1.1

0.5

R

28375142

5V7C (B:C)

H. sapiens LARP1-unique domain DM15

5'TOP motif

8

42

7.50x10^-6

298

7.5

-6.99

EMSA

1238

0.4

0.5

R

28379136

5WWX (A:C)

H. sapiens KH2 domain of MEX-3C

5-mer RNA

5

6

3.15x10^-6

293

7.5

-7.38

ITC

1380

0.8

0.9

R

28808060

5ZSC (A:C)

M. mulatta toll-like receptor 7

CCUUCA RNA

6

6

1.0x10^-7

298

5.5

-9.55

ITC

1227

0.5

0.5

R

30566863

6A6J (A:B)

D. rerio cold shock domain of Ybx1

6mer m5C RNA

6

6

2.23x10^-7

298

8.0

-9.07

ITC

1167

1.2

1.2

R

31399345

6GC5 (A:E)

H. sapiens HuR RRM3

AU-rich RNA

11

11

6.50x10^-7

298

7.0

-8.44

ITC

1264

0.7

0.8

R

30718402

6L1W (A:C)

M. musculus Zinc finger CCCH-type antiviral protein 1

CG rich RNA

7

7

1.20x10^-7

298

7.5

-9.44

ITC

1356

1.6

2

S

31914396

6LLB (A:C)

M. psychrophilus MPY-RNase J

6-mer RNA

6

5

4.0x10^-7

277

7.5

-8.11

EMSA

2527

0.8

0.7

R

28795788

6U9X (D:H)

T. brucei MERS1

G rich RNA

11

11

3.90x10^-8

298

7.5

-10.1

FP

2250

1.4

1.8

S

31704716

6L5N (A:C)

H. sapiens DEAD-box RNA helicase DDX21

poly(U)-15mer

15

15

2.90x10^-5

300

7.5

-6.23

MST

1201

1.4

1.2

R

32714761

6LT7 (AB:C)

H. sapiens RPP20-RPP25

P3 domain of lncRNA RMRP

50

50

7.69x10^-8

295

7.5

-9.6

EMSA

5371

1.6

1.6

S

20215441

6U6Y (AD:EH)

H. sapiens SAMHD1

ribo(CGCCU)-oligonucleotide

5

5

1.10x10^-7

300

8.0

-9.55

Fluorescence titration

1996

0.5

0.3

R

33531504

6WXY (BC:A)

T. succinifaciens card1 nuclease

cA6-bound

6

6

7.80x10^-8

293

7.5

-9.53

ITC

2186

0.5

0.6

R

33461211

7C45 (A:D)

T. brucei RNase D ribonuclease

gRNA U12

12

12

1.0x10^-6

277

8.0

-7.6

EMSA

2405

2.6

4.0

F

33332555

7DOL (A:C)

M. genitalium Ribonuclease R

ssRNA

6

24

6.62x10^-9

298

6.8

-11.15

FP

2076

1.0

0.9

R

33788943

7EIU (A:C)

S. pombe meiosis protein mei2 RRM3

8mer meiRNA

6

8

5.30x10^-7

293

6.5

-8.41

FP

2431

0.9

0.6

R

35512546

7L6T (A:C)

SARS-CoV-2 Nsp16/10 Heterodimer

mRNA capping

7

7

2.80x10^-5

298

8.0

-6.21

ITC

1120

0.6

1.0

R

34131072

7V4G (A:D)

H. sapiens RNA demethylase ALKBH5

m6A-containing ssRNA

8

11

5.29x10^-5

298

7.5

-5.83

MST

1529

0.6

0.7

R

27156733

7VKI (A:B)

H Sapiens ESRP1 Qrrm2

mRNA

12

6

6.75x10^-7

298

8.0

-8.41

ITC

632

1.5

1

R

38015468

8EDJ (A:R)

M. mulatta APOBEC3G

RA3G-ssRNA-GA

10

10

4.70x10^-8

277

7.5

-9.29

EMSA

1692

17.7

23.2

F

36470880

8AXF (ABCD:Q)

E. Fici nucleocapsid protein

ssRNA

42

42

1.76x10^-7

298

7.4

-9.21

ITC

10949

3.7

3.2

F

37039649

III. Bound-Unbound cases (5)

(B) Ribosomal proteins (1)

6AAX (A:B)

H. sapiens Mitochondrial transcription factor B1

12s rRNA

28

28

4.0x10^-7

310

8.0

-9.08

EMSA

1758

3.9

6.1

31251801

(C) Duplex RNA (4)

1HQ1 (A:B)

E. coli SRP

4.5S RNA domain IV

49

49

3.33x10^-11

300

7.5

-14.38

FBA

1364

38.3

30

11243816

2PJP (A:B)

E. coli SelB

SECIS RNA

23

23

3.0x10^-10

298

6.0

-12.98

EMSA

1300

2.5

3.6

17537456

3BT7 (A:C)

E. coli methyltransferase TrmA

T-arm analogue

19

19

2.0x10^-8

300

7.5

-10.57

FBA

2230

3.1

3.5

32597953

6HTU (ABC:DF)

H. sapiens hStau1 dsRBD3-4

ARF1 RNA

19

19

1.40x10^-8

277

9.7

-9.95

EMSA

3840

1.6

1.6

30456389