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- PDB-7pdv: Crystal structure of RBM5 RRM1-zinc finger in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 7pdv
TitleCrystal structure of RBM5 RRM1-zinc finger in complex with RNA
Components
  • RNA (5'-R(P*UP*GP*GP*CP*UP*CP*UP*UP*CP*U)-3')
  • RNA binding motif protein 5 isoform 1
KeywordsRNA BINDING PROTEIN / RRM domain / Zinc finger / Splicing
Function / homology
Function and homology information


spliceosomal complex / mRNA splicing, via spliceosome / RNA binding / metal ion binding
Similarity search - Function
RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type ...RNA-binding protein 5, RNA recognition motif 1 / RNA-binding protein 5, RNA recognition motif 2 / OCRE domain / OCRE domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA binding motif protein 5 isoform 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsSoni, K. / Jagtap, P.K.A. / Sattler, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for specific RNA recognition by the alternative splicing factor RBM5.
Authors: Soni, K. / Jagtap, P.K.A. / Martinez-Lumbreras, S. / Bonnal, S. / Geerlof, A. / Stehle, R. / Simon, B. / Valcarcel, J. / Sattler, M.
History
DepositionAug 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA binding motif protein 5 isoform 1
C: RNA binding motif protein 5 isoform 1
E: RNA binding motif protein 5 isoform 1
F: RNA (5'-R(P*UP*GP*GP*CP*UP*CP*UP*UP*CP*U)-3')
G: RNA binding motif protein 5 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0869
Polymers58,8255
Non-polymers2624
Water00
1
A: RNA binding motif protein 5 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9992
Polymers13,9331
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7950 Å2
MethodPISA
2
C: RNA binding motif protein 5 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9992
Polymers13,9331
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8100 Å2
MethodPISA
3
E: RNA binding motif protein 5 isoform 1
F: RNA (5'-R(P*UP*GP*GP*CP*UP*CP*UP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0903
Polymers17,0252
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-12 kcal/mol
Surface area9170 Å2
MethodPISA
4
G: RNA binding motif protein 5 isoform 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9992
Polymers13,9331
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.230, 65.890, 94.910
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RNA binding motif protein 5 isoform 1


Mass: 13933.171 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBM5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S2Z549
#2: RNA chain RNA (5'-R(P*UP*GP*GP*CP*UP*CP*UP*UP*CP*U)-3')


Mass: 3091.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M Sodium cacodylate, 18mM CaCl2, 2.7 mM spermine, 9% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.27982 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27982 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 3.49→47.45 Å / Num. obs: 14244 / % possible obs: 90.7 % / Redundancy: 1.803 % / CC1/2: 0.94 / Rmerge(I) obs: 0.288 / Rrim(I) all: 0.397 / Χ2: 0.727 / Net I/σ(I): 1.9 / Num. measured all: 25689 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.49-3.591.8250.9280.861863113810210.5361.26889.7
3.59-3.681.850.80911896114510250.5041.11189.5
3.68-3.791.8170.6171.291841111210130.6780.84591.1
3.79-3.911.7830.6631.06170810579580.6850.91290.6
3.91-4.041.7790.4361.53164210289230.8060.689.8
4.04-4.181.7360.4941.41163210599400.7790.67888.8
4.18-4.331.8190.3231.7614849398160.8870.44586.9
4.33-4.511.820.3561.8315789498670.8560.49491.4
4.51-4.711.8260.2811.8314798948100.9330.38990.6
4.71-4.941.7990.222.2913718197620.9460.30293
4.94-5.211.7860.2352.3113728247680.9260.32593.2
5.21-5.531.7360.2172.212227857040.9350.30189.7
5.53-5.911.8490.2672.1211856966410.9350.36992.1
5.91-6.381.8470.212.5212177046590.9390.29293.6
6.38-6.991.830.162.6610526025750.9610.22395.5
6.99-7.811.7640.1572.838915465050.9480.2292.5
7.81-9.021.8040.1163.287925114390.9830.16285.9
9.02-11.051.7980.0973.766874033820.9770.13594.8
11.05-15.631.7610.0893.675163292930.9740.12489.1
15.63-47.451.8250.0694.352611731430.9860.09682.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PCV

7pcv


Resolution: 3.49→47.45 Å / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 41.13 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.39 1066 7.48 %
Rwork0.3373 13242 -
obs0.3421 14244 90.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.52 Å2 / Biso mean: 31.4705 Å2 / Biso min: 11.52 Å2
Refinement stepCycle: final / Resolution: 3.49→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 138 4 0 3426
Biso mean--25.04 --
Num. residues----435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.49-3.680.4041460.32871858200483
3.68-3.910.33561270.31691898202585
3.91-4.210.39541480.31641851199982
4.21-4.630.37331370.33081906204384
4.63-5.30.40741520.33581909206186
5.3-6.680.35171520.34761919207185
6.68-47.450.4051400.37311901204185
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1568-0.0052-0.02290.0032-0.00410.01110.01080.0129-0.0422-0.00660.0132-0.0256-0.0179-0.01290.0797-0.07750.2053-0.07920.1694-0.28360.01913.9446-2.067722.8586
2-0.01860.0004-0.0087-0.0071-0.0016-0.01030.01550.00340.0862-0.01890.01860.0183-0.1331-0.04660.11-0.98790.19020.284-0.1109-0.2394-0.54424.5767-0.766818.8515
30.0007-0.0279-0.00110.3636-0.02550.04350.03320.05660.0297-0.0838-0.0176-0.0058-0.00470.00470.12780.10350.2351-0.08190.26090.01550.036821.99731.957727.9431
40.00080.02630.00570.1502-0.07680.2217-0.0232-0.00020.02030.00390.0048-0.0231-0.01320.0102-0.04770.0256-0.6654-0.15950.1297-0.0205-0.333419.2392-12.25930.7916
50.1103-0.0326-0.06420.0150.01230.0342-0.0208-0.01690.16980.0134-0.0194-0.0816-0.16410.0779-0.4143-0.5098-0.05420.73780.0703-0.2172-0.347517.16875.061926.4848
60.0015-00.03220.00540.00890.06830.03160.12160.0050.0430.0758-0.00310.08510.01820.721-0.21950.18560.08650.0857-0.0871-0.313314.78184.133714.9599
70.1856-0.07480.07950.06640.0560.2180.0281-0.0516-0.01240.03770.04930.06170.0375-0.07020.3029-0.3267-0.18060.17690.09760.29590.05978.68791.123222.8423
80.0320.03180.08720.1912-0.03780.2656-0.06330.0681-0.013-0.0424-0.05060.09060.02450.0845-0.7577-0.0375-0.1226-0.30090.28550.26730.05246.36744.073644.0085
90.1398-0.11280.01580.0818-0.01760.1334-0.0478-0.0203-0.0553-0.0180.07220.00390.05230.05640.2348-0.18970.09120.3379-0.02940.1839-0.097410.93050.459443.5128
100.0722-0.0076-0.14390.00680.02720.29630.00560.07630.0267-0.08440.02120.0051-0.0136-0.00320.06290.67060.00220.08260.33470.5740.415217.08263.791541.772
11-0.0143-0.00520.0054-0.00680.0002-0.01130.15290.0047-0.02320.06140.10790.0393-0.03310.02561.6293-0.86690.2265-0.3790.01290.2499-0.481129.1-0.693343.1086
120.3813-0.028-0.18730.00780.04570.16510.03690.10030.2334-0.0165-0.01630.0521-0.16430.0816-0.3531-0.70390.41121.01150.29040.0951-0.435733.3355-2.399635.7921
13-0.0001-0.002-0.0019-0.0034-0.0036-0.0050.01220.00170.0214-0.01260.01140.05840.0314-0.02970.2356-0.36820.01990.06280.03790.0547-0.069937.172411.214945.838
140.14780.07150.22050.03660.10720.3057-0.01770.00440.06170.02-0.0086-0.085-0.10120.17380.2310.17640.0513-0.2950.2958-0.10280.01336.0284-3.842952.7649
150.1112-0.05440.0660.1081-0.03030.03970.0168-0.0481-0.05330.09330.07280.02480.0079-0.00010.3635-0.18640.1928-0.077-0.08390.12160.023343.47871.480738.8006
160.0693-0.0754-0.12990.25080.14080.23860.0044-0.016-0.01690.0117-0.0239-0.0088-0.0251-0.0412-0.0405-0.14810.0272-0.0215-0.0053-0.25350.320347.8699-0.343619.4686
170.07940.06550.02650.0460.0150.10460.0386-0.0239-0.0320.06370.0216-0.0091-0.03390.01890.4464-0.2518-0.4680.37440.0911-0.2714-0.096939.83942.811920.4518
180.1041-0.04490.02990.1998-0.21890.24220.0258-0.06740.03960.07990.01510.0161-0.0723-0.00180.04540.6343-0.01320.14280.6048-0.07820.053533.65124.135423.7774
19-0.01290.01270.01950.05860.0632-0.01010.19970.2594-0.2777-0.20470.22480.12030.01750.12422.8841-1.7574-0.19920.30880.1542-0.4573-0.91595.357433.23816.3184
200.09180.1257-0.12380.1657-0.16850.1577-0.0031-0.02320.0225-0.01940.0312-0.0074-0.0024-0.00290.1548-0.27210.2949-0.19880.3271-0.41940.204310.92619.47681.9396
21-0.0636-0.0209-0.0184-0.1096-0.0581-0.0212-0.0067-0.0060.0731-0.0547-0.00990.04510.07260.0667-0.0367-1.39610.4718-0.2113-0.52790.6418-0.848915.283129.996212.9464
220.1267-0.05490.03560.15290.14090.20580.02150.02320.0433-0.1012-0.0118-0.0649-0.06930.0230.21540.2012-0.05120.18070.12330.0318-0.05237.982132.400315.1641
230.1018-0.1116-0.20760.16590.1080.69410.04530.0497-0.11460.0272-0.0354-0.00860.1298-0.25330.1257-0.0567-0.233-0.07280.4229-0.3202-0.192745.923737.558726.0946
240.2321-0.00580.03340.24420.26460.2728-0.05360.0303-0.0470.0102-0.0033-0.00890.01080.04-0.3812-0.75790.6058-0.09460.28560.58590.074850.237426.566630.5326
25-0.00470.00050.0051-0.0047-0.0006-0.0083-0.0053-0.03050.01560.0438-0.0178-0.0299-0.07360.0592-0.1874-0.2898-0.16690.16110.1007-0.1974-0.228242.70639.660617.7985
260.12150.0062-0.0184-0.008-0.0072-0.0066-0.01650.0561-0.03170.09320.01670.02410.10450.0848-0.0222-0.5933-0.1774-0.22820.29870.3631-0.025241.89721.392324.8457
270.42080.1480.19380.0520.05380.24990.0270.0424-0.0029-0.01560.00140.0110.022-0.00940.1341-0.1794-0.0629-0.12860.0419-0.23190.055137.468725.700535.4108
280.0091-0.02250.04390.0522-0.10150.19620.00640.0169-0.03530.0149-0.00390.01690.03270.016-0.0280.07020.203-0.1610.087-0.0590.041944.151135.743136.4296
290.0229-0.02550.00450.0214-0.00430.0050.0554-0.02220.0212-0.08620.0419-0.06580.0320.0450.4573-0.30630.00470.03510.1047-0.50240.077237.554332.877130.0226
300.0019-0.0082-0.01660.02980.07560.17440.0289-0.0279-0.00650.03410.0056-0.01710.003-0.00730.168-0.2062-0.01820.03140.1585-0.095-0.101227.56630.450213.1636
310.0484-0.16780.01780.9324-0.13270.14430.03370.0232-0.02390.0170.0624-0.03640.06690.0440.3868-0.1593-0.0938-0.0028-0.0346-0.28120.006729.242328.79984.3197
320.0090.0130.02420.0190.02540.0380.03520.00130.0111-0.09390.004-0.0256-0.0822-0.02420.3506-0.03380.0619-0.3419-0.055-0.0984-0.394136.506828.29125.8462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 14 )A8 - 14
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 34 )A15 - 34
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 40 )A35 - 40
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 49 )A41 - 49
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 59 )A50 - 59
6X-RAY DIFFRACTION6chain 'A' and (resid 60 through 78 )A60 - 78
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 88 )A79 - 88
8X-RAY DIFFRACTION8chain 'A' and (resid 89 through 98 )A89 - 98
9X-RAY DIFFRACTION9chain 'A' and (resid 99 through 108 )A99 - 108
10X-RAY DIFFRACTION10chain 'A' and (resid 109 through 114 )A109 - 114
11X-RAY DIFFRACTION11chain 'C' and (resid 8 through 40 )C8 - 40
12X-RAY DIFFRACTION12chain 'C' and (resid 41 through 59 )C41 - 59
13X-RAY DIFFRACTION13chain 'C' and (resid 60 through 69 )C60 - 69
14X-RAY DIFFRACTION14chain 'C' and (resid 70 through 79 )C70 - 79
15X-RAY DIFFRACTION15chain 'C' and (resid 80 through 89 )C80 - 89
16X-RAY DIFFRACTION16chain 'C' and (resid 90 through 94 )C90 - 94
17X-RAY DIFFRACTION17chain 'C' and (resid 95 through 109 )C95 - 109
18X-RAY DIFFRACTION18chain 'C' and (resid 110 through 114 )C110 - 114
19X-RAY DIFFRACTION19chain 'E' and (resid 8 through 58 )E8 - 58
20X-RAY DIFFRACTION20chain 'E' and (resid 59 through 66 )E59 - 66
21X-RAY DIFFRACTION21chain 'E' and (resid 67 through 114 )E67 - 114
22X-RAY DIFFRACTION22chain 'F' and (resid 2 through 8 )F2 - 8
23X-RAY DIFFRACTION23chain 'G' and (resid 8 through 23 )G8 - 23
24X-RAY DIFFRACTION24chain 'G' and (resid 24 through 36 )G24 - 36
25X-RAY DIFFRACTION25chain 'G' and (resid 37 through 52 )G37 - 52
26X-RAY DIFFRACTION26chain 'G' and (resid 53 through 66 )G53 - 66
27X-RAY DIFFRACTION27chain 'G' and (resid 67 through 71 )G67 - 71
28X-RAY DIFFRACTION28chain 'G' and (resid 72 through 76 )G72 - 76
29X-RAY DIFFRACTION29chain 'G' and (resid 77 through 86 )G77 - 86
30X-RAY DIFFRACTION30chain 'G' and (resid 87 through 91 )G87 - 91
31X-RAY DIFFRACTION31chain 'G' and (resid 92 through 96 )G92 - 96
32X-RAY DIFFRACTION32chain 'G' and (resid 97 through 114 )G97 - 114

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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