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- PDB-4wnl: The X-ray structure of a RNA-binding protein complex -

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Open data


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Basic information

Entry
Database: PDB / ID: 4wnl
TitleThe X-ray structure of a RNA-binding protein complex
Components
  • SWI5-dependent HO expression protein 2
  • SWI5-dependent HO expression protein 3
KeywordsRNA BINDING PROTEIN / RNA-binding / mRNA transport
Function / homology
Function and homology information


mating type switching / endoplasmic reticulum inheritance / cellular bud tip / intracellular mRNA localization / sequence-specific mRNA binding / mRNA transport / mRNA binding / lipid binding / endoplasmic reticulum membrane / RNA binding ...mating type switching / endoplasmic reticulum inheritance / cellular bud tip / intracellular mRNA localization / sequence-specific mRNA binding / mRNA transport / mRNA binding / lipid binding / endoplasmic reticulum membrane / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
She2 domain / RNA binding protein She2 / She2 domain superfamily / RNA binding protein She2p / SWI5-dependent HO expression protein 3 / SWI5-dependent HO expression protein 3 / Fumarase C; Chain A, domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / SWI5-dependent HO expression protein 3 / SWI5-dependent HO expression protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsSingh, N. / Blobel, G. / Shi, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10RR027037-01 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Hooking She3p onto She2p for myosin-mediated cytoplasmic mRNA transport.
Authors: Singh, N. / Blobel, G. / Shi, H.
History
DepositionOct 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_related.content_type / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 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
C: SWI5-dependent HO expression protein 2
A: SWI5-dependent HO expression protein 2
B: SWI5-dependent HO expression protein 2
D: SWI5-dependent HO expression protein 2
E: SWI5-dependent HO expression protein 3
F: SWI5-dependent HO expression protein 3
G: SWI5-dependent HO expression protein 3
H: SWI5-dependent HO expression protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,63420
Polymers120,5778
Non-polymers1,05712
Water00
1
C: SWI5-dependent HO expression protein 2
A: SWI5-dependent HO expression protein 2
F: SWI5-dependent HO expression protein 3
G: SWI5-dependent HO expression protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7259
Polymers60,2884
Non-polymers4365
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-54 kcal/mol
Surface area20760 Å2
MethodPISA
2
B: SWI5-dependent HO expression protein 2
D: SWI5-dependent HO expression protein 2
E: SWI5-dependent HO expression protein 3
H: SWI5-dependent HO expression protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,90911
Polymers60,2884
Non-polymers6217
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-69 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.620, 64.670, 116.370
Angle α, β, γ (deg.)90.00, 117.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
SWI5-dependent HO expression protein 2


Mass: 26721.229 Da / Num. of mol.: 4 / Mutation: C14S, C68S, C180S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SHE2, YKL130C / Production host: Escherichia coli (E. coli) / References: UniProt: P36068
#2: Protein/peptide
SWI5-dependent HO expression protein 3


Mass: 3422.953 Da / Num. of mol.: 4 / Fragment: unp residues 342-374 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: B5VE90
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: Tri-sodium citrate, pH 6.4, 13% (w/v) PEG 4K, 100mM (NH4)2SO4 and 3% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.8→83.54 Å / Num. obs: 28752 / % possible obs: 99.9 % / Redundancy: 6.8 % / Net I/σ(I): 12.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1678) / Classification: refinement
RefinementResolution: 2.8→59.692 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 1388 4.88 %
Rwork0.2123 --
obs0.2143 28450 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→59.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7492 0 64 0 7556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027704
X-RAY DIFFRACTIONf_angle_d0.57910421
X-RAY DIFFRACTIONf_dihedral_angle_d13.5452789
X-RAY DIFFRACTIONf_chiral_restr0.0211226
X-RAY DIFFRACTIONf_plane_restr0.0021291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90010.34291240.30042643X-RAY DIFFRACTION97
2.9001-3.01620.34081560.30642645X-RAY DIFFRACTION98
3.0162-3.15350.32331420.30192653X-RAY DIFFRACTION99
3.1535-3.31970.27511330.26572699X-RAY DIFFRACTION99
3.3197-3.52770.30541290.22642711X-RAY DIFFRACTION99
3.5277-3.80.26311280.21492728X-RAY DIFFRACTION100
3.8-4.18230.22821440.19542716X-RAY DIFFRACTION99
4.1823-4.78730.22221290.17712705X-RAY DIFFRACTION100
4.7873-6.03060.25351520.19822750X-RAY DIFFRACTION99
6.0306-59.70590.20491510.16852812X-RAY DIFFRACTION99
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)
11.70310.54810.54021.73440.20731.9415-0.20050.5602-0.8004-0.42740.2696-0.63690.23440.125-0.04720.43520.01190.17940.4703-0.15980.6153-10.608323.032317.971
27.03624.74532.94296.73433.18643.73390.95160.1088-0.8293-0.8314-0.44170.20480.8874-0.6791-0.61880.796-0.1521-0.00480.7591-0.06950.7163-33.62723.389719.1286
32.39822.09480.4333.26260.26182.3444-0.2641-0.1887-0.2421-0.3194-0.14310.20490.2428-0.35620.14530.36180.03220.16620.5406-0.15370.5464-20.917326.439920.0805
43.10243.17630.54683.7921-0.35981.17150.09110.3561-0.3853-0.28710.1023-0.41470.15-0.17180.05440.4117-0.04590.08770.4202-0.11420.4225-1.887244.831615.3933
53.45343.340.01984.87690.0373.0874-0.18860.39530.1507-0.14120.16840.5082-0.2438-0.7850.08940.4146-0.02260.1140.6337-0.1190.4844-27.413332.752515.4306
63.91681.6317-0.00082.5652-0.84660.3604-0.76320.56941.5256-0.67380.31081.9417-0.6147-1.6274-0.03050.8530.1564-0.22691.34030.28451.2447-36.593343.15577.766
73.04622.9214-0.27414.5856-0.25871.8346-0.45060.83170.3184-0.60150.42891.53650.1398-0.79530.1060.3896-0.06060.03080.9477-0.09040.7516-36.109728.223510.1795
82.70590.4213-0.26382.4504-0.37943.4783-0.5971.5102-1.2174-0.65430.6648-0.74680.09650.4228-0.05930.5216-0.03010.09760.6819-0.25350.5265-15.755225.89225.6104
93.87860.3043-0.48142.5056-0.11172.9826-0.34361.01050.8232-0.73210.40420.5936-0.11-0.3635-0.0260.47290.139-0.11170.4640.12830.513.725117.625912.7048
102.58221.5182-1.00731.84230.58761.9963-0.19930.18540.9202-0.60050.21141.1259-0.27-0.44450.00550.3460.0519-0.11410.47550.08940.6248.414214.342321.9176
112.00772.5425-3.35688.7647-1.22122.83770.92140.78121.2938-0.7610.5883-0.45521.01190.3838-1.2120.8332-0.0682-0.05320.6777-0.05810.675533.603134.334417.7236
120.15861.16-1.03624.0183-0.0212.17040.1667-0.1608-0.18070.2243-0.2858-0.6866-0.0683-0.020.13190.26750.0315-0.0730.45130.06660.568421.787912.604518.6945
134.30543.7913-2.61835.5831-1.27151.9964-0.38170.40330.152-0.62750.22380.35560.25380.51950.01920.4351-0.0209-0.0120.5328-0.01160.3632.309-5.687815.1658
142.15222.543-0.68753.94530.47170.53050.24-0.6433-0.26860.0748-0.5744-0.46860.06140.01290.22320.3804-0.0154-0.04280.51430.10470.35423.11997.9649.6819
152.79844.099-0.61966.60021.214.0818-0.0834-0.3108-0.6276-0.13270.1546-1.25820.76540.6808-0.17760.48780.1156-0.08980.52840.12430.565433.324.648518.9903
166.5151-2.6444-2.07168.5003-1.33036.0390.32260.9748-0.83830.3159-1.2143-1.29940.93822.44670.57120.80760.051-0.05061.2618-0.12241.251736.2001-4.10787.5904
175.52920.8120.08729.03420.56766.4717-0.00090.4835-0.3187-0.6539-0.1503-2.02540.3251.0899-0.04740.50690.11190.01870.64870.13450.716636.578610.40758.0806
183.10660.5531-0.2573.2099-0.50723.502-0.1670.6780.6399-0.53660.11780.4382-0.0887-0.4102-0.04910.42030.1313-0.07040.67510.14930.412816.76213.11384.3744
192.0061-2.6771-1.269.3952-1.80587.36240.2856-1.1012-0.15050.2761-0.49131.8534-0.0629-0.2168-0.20370.5074-0.30380.14170.8391-0.28760.753-39.173511.523138.1566
200.44410.38170.13392.3676-0.86662.59630.7486-0.4950.84341.0081-0.4960.9587-0.5883-0.0602-0.17790.51030.0670.22090.3948-0.16240.6082-23.059437.441338.4549
214.36812.10970.10193.1747-0.44990.47320.24690.29510.4320.1144-0.06040.6359-0.2041-0.2799-0.17640.42710.09790.08610.4848-0.11010.468-22.236838.922729.3177
223.80052.44260.12452.9416-1.07892.8347-0.15020.2103-0.3359-0.12970.1690.31070.1614-0.1433-0.02990.34840.00360.1410.4196-0.10230.574-25.036823.450732.3399
232.7497-0.22840.64030.2260.75973.98910.1652-0.0362-0.23140.07680.2184-0.5247-0.16390.1304-0.40890.4448-0.093-0.00960.4405-0.04470.4898-1.517444.179936.8774
241.36291.61520.75753.9741.79121.57390.18540.1877-0.31120.48340.0848-0.22620.18720.1018-0.30860.40990.0090.0940.4285-0.07790.4801-17.491721.159138.1385
257.451-0.41833.81771.671-2.89582.03130.02341.2307-1.7773-0.8195-0.7191-1.54631.92522.01810.78790.6178-0.00780.22240.6054-0.0511.1848-6.021614.420432.5939
264.20111.116-0.6892.7631-1.12492.49380.5216-0.7243-1.45360.8104-0.6773-0.38320.52780.08710.17780.7575-0.0280.10310.360.02660.9603-15.714711.50242.5156
273.10620.3967-0.75572.8598-0.87972.76980.2791-0.42240.19820.4408-0.29430.4922-0.70020.0981-0.07580.57060.03220.11560.4996-0.03730.3955-20.963530.677946.5951
281.78250.734-0.19923.39140.55972.33880.2532-0.2387-0.19350.4545-0.262-0.69250.01590.5372-0.02680.3801-0.0263-0.16710.48190.10270.453225.27477.110832.2853
296.24423.7268-0.32276.7571-0.16716.0545-0.24-0.0485-0.19280.76940.19370.8584-0.04920.19880.14510.5572-0.00980.10410.3339-0.0850.46532.675-4.354336.6143
300.86790.5623-1.27673.12210.24851.92580.2636-0.28180.12061.166-0.2533-0.2656-0.3963-0.153-0.0930.5257-0.0553-0.13950.50180.02090.372719.02218.404136.6966
318.65813.6992.52036.29392.60255.60450.3555-0.71841.61051.1793-0.39821.14290.2936-0.4664-0.04860.8336-0.01370.02320.3494-0.04040.75898.781125.375435.5967
325.06911.9447-0.19825.1847-0.50592.941-0.0457-0.78450.08030.4117-0.145-0.76960.14440.3030.06170.6974-0.074-0.1740.6347-0.05040.381223.368212.377944.7404
339.3449-0.0279-5.07314.6876-2.50414.93070.9031-1.25140.75760.3875-0.31080.5543-0.1938-1.1039-0.66990.834-0.0336-0.08010.7604-0.1520.500617.685726.681646.5327
345.63792.9871-0.69897.2205-1.19980.9950.59381.38110.7589-0.6415-0.70111.31330.11240.0354-0.20220.7971-0.304-0.09640.9706-0.07420.8523-33.350330.36553.2018
356.5205-0.9323-2.7659.24160.03873.3460.39060.4632-0.56871.4126-1.1764-1.2437-0.05781.32890.52170.82250.040.16420.76140.19940.8107-16.355212.895348.1387
361.8916-0.7576-1.27455.46281.66572.265-0.34840.1755-0.5908-0.246-0.256-0.9932-0.26010.54690.03470.10111.24460.9331.6983-0.24740.497333.73719.8252.2392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND RESID 8:78 )C8 - 78
2X-RAY DIFFRACTION2( CHAIN C AND RESID 79:93 )C79 - 93
3X-RAY DIFFRACTION3( CHAIN C AND RESID 94:120 )C94 - 120
4X-RAY DIFFRACTION4( CHAIN C AND RESID 121:139 )C121 - 139
5X-RAY DIFFRACTION5( CHAIN C AND RESID 140:186 )C140 - 186
6X-RAY DIFFRACTION6( CHAIN C AND RESID 187:195 )C187 - 195
7X-RAY DIFFRACTION7( CHAIN C AND RESID 196:206 )C196 - 206
8X-RAY DIFFRACTION8( CHAIN C AND RESID 207:239 )C207 - 239
9X-RAY DIFFRACTION9( CHAIN A AND RESID 8:46 )A8 - 46
10X-RAY DIFFRACTION10( CHAIN A AND RESID 47:78 )A47 - 78
11X-RAY DIFFRACTION11( CHAIN A AND RESID 79:93 )A79 - 93
12X-RAY DIFFRACTION12( CHAIN A AND RESID 94:120 )A94 - 120
13X-RAY DIFFRACTION13( CHAIN A AND RESID 121:139 )A121 - 139
14X-RAY DIFFRACTION14( CHAIN A AND RESID 140:163 )A140 - 163
15X-RAY DIFFRACTION15( CHAIN A AND RESID 164:185 )A164 - 185
16X-RAY DIFFRACTION16( CHAIN A AND RESID 186:195 )A186 - 195
17X-RAY DIFFRACTION17( CHAIN A AND RESID 196:206 )A196 - 206
18X-RAY DIFFRACTION18( CHAIN A AND RESID 207:238 )A207 - 238
19X-RAY DIFFRACTION19( CHAIN B AND RESID 8:14 )B8 - 14
20X-RAY DIFFRACTION20( CHAIN B AND RESID 15:46 )B15 - 46
21X-RAY DIFFRACTION21( CHAIN B AND RESID 47:79 )B47 - 79
22X-RAY DIFFRACTION22( CHAIN B AND RESID 80:120 )B80 - 120
23X-RAY DIFFRACTION23( CHAIN B AND RESID 121:139 )B121 - 139
24X-RAY DIFFRACTION24( CHAIN B AND RESID 140:173 )B140 - 173
25X-RAY DIFFRACTION25( CHAIN B AND RESID 174:185 )B174 - 185
26X-RAY DIFFRACTION26( CHAIN B AND RESID 191:206 )B191 - 206
27X-RAY DIFFRACTION27( CHAIN B AND RESID 207:238 )B207 - 238
28X-RAY DIFFRACTION28( CHAIN D AND RESID 8:120 )D8 - 120
29X-RAY DIFFRACTION29( CHAIN D AND RESID 121:139 )D121 - 139
30X-RAY DIFFRACTION30( CHAIN D AND RESID 140:173 )D140 - 173
31X-RAY DIFFRACTION31( CHAIN D AND RESID 174:200 )D174 - 200
32X-RAY DIFFRACTION32( CHAIN D AND RESID 201:238 )D201 - 238
33X-RAY DIFFRACTION33( CHAIN E AND RESID 362:369 )E362 - 369
34X-RAY DIFFRACTION34( CHAIN F AND RESID 362:369 )F362 - 369
35X-RAY DIFFRACTION35( CHAIN G AND RESID 362:369 )G362 - 369
36X-RAY DIFFRACTION36( CHAIN H AND RESID 363:368 )H363 - 368

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