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- PDB-4wan: Crystal structure of Msl5 protein in complex with RNA at 1.8 A -

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Basic information

Entry
Database: PDB / ID: 4wan
TitleCrystal structure of Msl5 protein in complex with RNA at 1.8 A
Components
  • Branchpoint-bridging protein
  • RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
KeywordsPROTEIN BINDING/RNA / Msl5 / BBP / RNA binding / yeast pre-mRNA splicing / PROTEIN BINDING-RNA complex
Function / homology
Function and homology information


pre-mRNA branch point binding / regulation of mRNA splicing, via spliceosome / commitment complex / spliceosomal complex assembly / mRNA splicing, via spliceosome / mRNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / KH domain-containing BBP-like / K Homology domain, type 1 / Clathrin adaptor, appendage, Ig-like subdomain superfamily / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily ...Splicing factor 1, helix-hairpin domain / : / Splicing factor 1 helix-hairpin domain / KH domain-containing BBP-like / K Homology domain, type 1 / Clathrin adaptor, appendage, Ig-like subdomain superfamily / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / RNA / RNA (> 10) / Branchpoint-bridging protein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJacewicz, A. / Smith, P. / Chico, L. / Schwer, B. / Shuman, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM52470 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM50288 United States
CitationJournal: Rna / Year: 2015
Title: Structural basis for recognition of intron branchpoint RNA by yeast Msl5 and selective effects of interfacial mutations on splicing of yeast pre-mRNAs.
Authors: Jacewicz, A. / Chico, L. / Smith, P. / Schwer, B. / Shuman, S.
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Branchpoint-bridging protein
B: RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
C: Branchpoint-bridging protein
D: RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
E: Branchpoint-bridging protein
F: RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
G: Branchpoint-bridging protein
H: RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,62119
Polymers71,6588
Non-polymers96311
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-95 kcal/mol
Surface area28370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.380, 130.970, 53.370
Angle α, β, γ (deg.)90.00, 117.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 8 molecules ACEGBDFH

#1: Protein
Branchpoint-bridging protein / Mud synthetic-lethal 5 protein / Splicing factor 1 / Zinc finger protein BBP


Mass: 14455.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MSL5, BBP, SF1, YLR116W, L2949 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q12186
#2: RNA chain
RNA (5'-R(P*UP*AP*CP*UP*AP*AP*CP*A)-3')


Mass: 3459.138 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Non-polymers , 4 types, 488 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 2.1-2.3 M ammonium sulfate, 0.01 M magnesium acetate, 0.05 M MES
PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.072 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.8→45.61 Å / Num. obs: 59297 / % possible obs: 99.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.4 / % possible all: 95.4

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.61 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.57 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3010 5.08 %RANDOM
Rwork0.175 ---
obs0.18 59249 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 627 58 477 4896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014554
X-RAY DIFFRACTIONf_angle_d1.0656270
X-RAY DIFFRACTIONf_dihedral_angle_d15.0651866
X-RAY DIFFRACTIONf_chiral_restr0.045723
X-RAY DIFFRACTIONf_plane_restr0.004716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8041-1.83520.3061410.32522606X-RAY DIFFRACTION86
1.8352-1.86860.34031470.31272663X-RAY DIFFRACTION91
1.8686-1.90460.33891330.29532858X-RAY DIFFRACTION95
1.9046-1.94340.30721340.28852814X-RAY DIFFRACTION95
1.9434-1.98570.2771410.27682847X-RAY DIFFRACTION95
1.9857-2.03190.27971390.2612781X-RAY DIFFRACTION95
2.0319-2.08270.28511460.26182849X-RAY DIFFRACTION95
2.0827-2.1390.26481490.24762878X-RAY DIFFRACTION95
2.139-2.20190.25121490.23862799X-RAY DIFFRACTION95
2.2019-2.27290.22031420.23382804X-RAY DIFFRACTION95
2.2729-2.35420.24231620.22582830X-RAY DIFFRACTION95
2.3542-2.44840.25781360.22572845X-RAY DIFFRACTION95
2.4484-2.55980.22761810.21872805X-RAY DIFFRACTION94
2.5598-2.69470.22221550.22182813X-RAY DIFFRACTION95
2.6947-2.86340.24051650.20222806X-RAY DIFFRACTION94
2.8634-3.08430.20581440.17242849X-RAY DIFFRACTION95
3.0843-3.39440.19391600.14952826X-RAY DIFFRACTION95
3.3944-3.8850.15431370.11832849X-RAY DIFFRACTION95
3.885-4.8920.13121600.09332863X-RAY DIFFRACTION95
4.892-32.74790.1751670.12472858X-RAY DIFFRACTION94
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)
18.195-7.66632.00482.2549-1.78811.85080.0738-0.3046-0.1062-0.27760.1688-0.14030.14840.2894-0.31720.1690.03710.04130.2033-0.04920.263110.41610.664316.939
27.8003-2.5866-1.81057.65182.31366.9610.3739-0.12640.31840.0691-0.20960.2817-0.3765-0.5611-0.19460.13230.00940.03870.13540.00420.1474-1.08724.66929.0797
35.7014-2.52778.00371.0851-3.15742.05350.05140.67380.0248-0.1977-0.3236-0.4165-0.00931.23440.30350.26370.01480.14260.26190.03360.294414.458620.81193.026
42.99341.48853.97611.82971.8666.41210.02390.0325-0.04980.00420.02480.04420.0852-0.0048-0.01420.12940.00550.04570.09450.03550.14243.392711.11357.2864
52.3066-8.47175.82748.1758-6.69897.663-0.5179-0.56070.51060.34280.3604-0.7982-0.4845-0.26720.21440.1852-0.01640.01970.2179-0.03520.278111.440722.671816.4096
60.04890.0112-0.00750.0014-0.00420.0030.04950.60011.1049-0.6078-0.03380.3073-0.9709-0.6049-0.06611.18990.1660.13560.2122-0.00970.49112.874137.37128.4829
76.30440.9832-2.71152.1154-1.65718.56610.36870.5180.6573-0.43030.1082-0.2567-1.22070.1405-0.37750.44570.0490.14710.24460.03530.28318.82532.2084-5.4991
84.50371.15252.39793.4997-2.58836.47980.11470.22180.6109-0.4287-0.094-0.0608-0.5217-0.35430.01520.28830.08270.10480.20180.0020.22314.74724.0121-2.1113
93.3236-0.23951.14783.9419-1.72952.6050.0404-0.1966-0.2920.2516-0.01370.1989-0.1576-0.141-0.03820.10080.01530.03170.1144-0.00450.16017.763861.002813.484
102.5953-0.57160.56112.38191.96135.16990.05410.2474-0.0583-0.0683-0.0164-0.2745-0.10820.2498-0.04970.0947-0.030.03080.10570.02350.203917.46164.368813.569
114.24441.59462.08186.63961.55225.4497-0.05540.04620.6383-0.12-0.04730.3304-0.4522-0.41650.0810.16320.02640.05640.16650.01590.20659.479271.874118.7445
121.24290.4338-0.34524.7761-5.1129.46770.0318-0.0215-0.1688-0.6481-0.1358-0.14370.6075-0.08390.11740.10490.02950.03420.1528-0.01860.22988.450960.42654.7371
133.3248-1.4662-2.97927.82335.3494.93440.2473-2.4857-2.34341.81661.24710.46241.3883-0.1534-1.36440.53760.14-0.16540.71590.24530.813610.902942.662216.6015
143.2676-1.2065-0.53245.1481-0.36439.74770.01410.0221-1.2469-0.46490.0925-0.15140.73750.1505-0.10920.2280.0060.00610.1341-0.00090.472524.085648.431515.6138
152.0102-7.6194-2.3367.4068-2.24076.93180.2243-0.3878-1.0061-0.1119-0.5253-1.49831.07280.70510.24130.5873-0.0922-0.16070.46860.22370.990331.771645.38920.9756
168.7087-4.5599-0.23033.392.69436.78540.1505-0.7105-0.74170.36040.16380.29560.93630.6189-0.34410.22030.033-0.05610.25190.06770.288321.327454.896119.2946
173.35745.2521.15489.16794.48947.61810.2257-0.03460.8566-0.2425-0.36450.681-0.3813-0.50880.19460.1539-0.04660.10850.24630.06070.4019-5.386267.91177.7751
184.62972.38971.37893.7534-0.14932.5701-0.08650.4509-0.2677-0.148-0.0790.27260.1431-0.19840.15210.1406-0.0110.01320.1681-0.0450.2511-10.672552.16216.7937
194.07271.35112.25755.81323.04988.4652-0.12380.50210.0637-0.7287-0.16781.11-0.2152-1.15260.25680.1939-0.0394-0.08380.28660.05440.449-12.805958.89020.0232
200.16530.97831.0655.73146.19396.6847-0.2020.6810.4951-0.9617-0.82890.5516-0.248-1.09271.04411.1304-0.1008-0.36660.50870.02221.2344-16.85862.7322-6.8002
215.6379-1.5569-0.27147.04680.73264.06630.09520.28880.2898-0.27050.06560.1156-0.2190.0808-0.17550.0923-0.02020.05340.17890.03670.2284-5.986660.10029.867
224.98251.00321.31024.10590.28214.4255-0.0017-0.1214-0.83420.2702-0.27680.26940.6026-0.59380.23840.2592-0.09240.08570.2325-0.07290.4912-16.667439.75739.954
239.68381.27980.97670.89121.42499.0267-0.34390.8728-0.4502-0.6266-0.13840.70551.1415-0.39810.33080.2296-0.11210.04080.3517-0.05780.4298-16.999645.86193.7697
243.92261.6335-2.03767.5363-1.33375.5084-0.0975-0.0418-0.0108-0.04690.3563-0.6073-0.20210.4373-0.24260.14980.00740.02440.2144-0.06610.19115.686424.920227.358
252.274-0.08250.65485.91215.30575.73360.009-0.12760.13320.6909-0.28310.52570.4375-0.26870.25790.28760.01630.13780.24120.00630.2169-4.297922.499135.1857
267.03313.14534.95167.19810.66913.89510.3151-0.58610.40580.3662-0.553-0.0752-0.0747-0.23750.18730.48350.1489-0.140.6938-0.09170.333412.384823.438834.7541
271.10462.5906-0.3257.4393-1.16220.20960.4885-0.0156-0.6006-0.0798-0.1732-0.04730.7853-0.6208-0.31960.9595-0.1495-0.12010.9267-0.52260.87818.059920.509942.7123
280.1886-1.0907-0.63045.55323.3382.0171-0.6367-2.0866-0.26892.09831.2024-0.64891.38580.796-0.47050.73020.3862-0.11291.1248-0.42730.667412.80517.302734.0681
293.84121.4575-0.79972.8324-1.60592.8785-0.25020.0926-0.06960.20080.24760.26210.0228-0.3580.0070.23050.03580.10370.2322-0.03370.1743-2.667220.485124.9409
306.5088-4.1976-1.05026.5716-5.11088.8184-0.1776-0.38031.49210.89791.0259-2.2225-1.05152.8656-0.76620.6413-0.0804-0.13930.663-0.26720.6492-0.955541.930125.1372
313.55430.6477-0.70146.7351.28026.83420.2549-0.23450.4673-0.48490.23540.2875-1.4056-0.3378-0.33940.43290.02210.12590.2045-0.04530.3269-5.148138.630337.9405
321.99948.8824-4.27738.33-0.90732.0054-0.04890.42660.89691.24210.54571.4227-2.0617-0.8687-0.35220.88730.29180.41250.66630.25770.6415-5.224346.199743.9697
336.4258-4.4446-1.00935.8494.5059.4301-0.1841-0.50510.50710.43780.31530.0668-0.44160.2105-0.16720.22720.04530.05450.3176-0.07770.24511.235433.096339.0692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 145 THROUGH 153 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 154 THROUGH 170 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 171 THROUGH 183 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 184 THROUGH 223 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 224 THROUGH 242 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 243 THROUGH 249 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 250 THROUGH 268 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 3 THROUGH 10 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 145 THROUGH 170 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 171 THROUGH 203 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 204 THROUGH 215 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 216 THROUGH 242 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 243 THROUGH 249 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 250 THROUGH 262 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 263 THROUGH 269 )
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 2 THROUGH 10 )
17X-RAY DIFFRACTION17CHAIN 'E' AND (RESID 146 THROUGH 153 )
18X-RAY DIFFRACTION18CHAIN 'E' AND (RESID 154 THROUGH 183 )
19X-RAY DIFFRACTION19CHAIN 'E' AND (RESID 184 THROUGH 200 )
20X-RAY DIFFRACTION20CHAIN 'E' AND (RESID 201 THROUGH 210 )
21X-RAY DIFFRACTION21CHAIN 'E' AND (RESID 211 THROUGH 243 )
22X-RAY DIFFRACTION22CHAIN 'E' AND (RESID 244 THROUGH 267 )
23X-RAY DIFFRACTION23CHAIN 'F' AND (RESID 2 THROUGH 10 )
24X-RAY DIFFRACTION24CHAIN 'G' AND (RESID 147 THROUGH 170 )
25X-RAY DIFFRACTION25CHAIN 'G' AND (RESID 171 THROUGH 190 )
26X-RAY DIFFRACTION26CHAIN 'G' AND (RESID 191 THROUGH 195 )
27X-RAY DIFFRACTION27CHAIN 'G' AND (RESID 196 THROUGH 206 )
28X-RAY DIFFRACTION28CHAIN 'G' AND (RESID 207 THROUGH 215 )
29X-RAY DIFFRACTION29CHAIN 'G' AND (RESID 216 THROUGH 243 )
30X-RAY DIFFRACTION30CHAIN 'G' AND (RESID 244 THROUGH 249 )
31X-RAY DIFFRACTION31CHAIN 'G' AND (RESID 250 THROUGH 263 )
32X-RAY DIFFRACTION32CHAIN 'G' AND (RESID 264 THROUGH 268 )
33X-RAY DIFFRACTION33CHAIN 'H' AND (RESID 3 THROUGH 10 )

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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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