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- PDB-4z3u: PRV nuclear egress complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4z3u
TitlePRV nuclear egress complex
Components
  • UL31
  • UL34 protein
KeywordsVIRAL PROTEIN / complex / membrane binding
Function / homology
Function and homology information


viral budding from nuclear membrane / host cell nuclear inner membrane / host cell membrane / host cell nucleus / zinc ion binding / membrane
Similarity search - Function
Herpesvirus viron egress-type / Herpesvirus virion protein U34 / Herpesvirus UL31 / Herpesvirus UL31-like protein
Similarity search - Domain/homology
UL34 protein / UL34 / Nuclear egress lamina protein
Similarity search - Component
Biological speciesSuid herpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.706 Å
AuthorsBigalke, J.M. / Heldwein, E.E.
Funding support United States, Germany, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM111795-01 United States
Burroughs Wellcome Fund
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI097573-01A1 United States
German Research Foundation (DFG)BI 1658/1-1 Germany
CitationJournal: Embo J. / Year: 2015
Title: Structural basis of membrane budding by the nuclear egress complex of herpesviruses.
Authors: Bigalke, J.M. / Heldwein, E.E.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UL34 protein
B: UL31
C: UL34 protein
D: UL31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,34012
Polymers98,0094
Non-polymers3318
Water68538
1
A: UL34 protein
B: UL31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1766
Polymers49,0052
Non-polymers1724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-44 kcal/mol
Surface area20330 Å2
MethodPISA
2
C: UL34 protein
D: UL31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1646
Polymers49,0052
Non-polymers1594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-53 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.456, 125.456, 109.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsheterodimer in solution (confirmed by gel filtration and MALS)

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein UL34 protein


Mass: 20244.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid herpesvirus 1 / Gene: UL34 / Production host: Escherichia coli (E. coli) / References: UniProt: G3G8R3, UniProt: G3G8X8*PLUS
#2: Protein UL31 / UL31 protein


Mass: 28760.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid herpesvirus 1 / Gene: UL31 / Production host: Escherichia coli (E. coli) / References: UniProt: G3G955

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Non-polymers , 4 types, 46 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.3 M NaSCN, 18% PEG3350, 0.3 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.706→49.907 Å / Num. obs: 24223 / % possible obs: 99.36 % / Redundancy: 4.55 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.41
Reflection shellResolution: 2.706→2.802 Å / Redundancy: 4.21 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2.02 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIXphasing
PHENIXmodel building
SHELXphasing
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.706→49.907 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2725 1995 8.24 %
Rwork0.2121 --
obs0.2171 24223 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.706→49.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6554 0 8 38 6600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036713
X-RAY DIFFRACTIONf_angle_d0.7879107
X-RAY DIFFRACTIONf_dihedral_angle_d12.6832486
X-RAY DIFFRACTIONf_chiral_restr0.0281007
X-RAY DIFFRACTIONf_plane_restr0.0031199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.706-2.77340.39641350.31741510X-RAY DIFFRACTION96
2.7734-2.84840.32131390.30261546X-RAY DIFFRACTION100
2.8484-2.93220.37481400.29461561X-RAY DIFFRACTION100
2.9322-3.02680.34591410.28421566X-RAY DIFFRACTION100
3.0268-3.1350.29591410.291571X-RAY DIFFRACTION100
3.135-3.26050.311420.26341571X-RAY DIFFRACTION100
3.2605-3.40880.31571410.24161574X-RAY DIFFRACTION100
3.4088-3.58850.29391420.22691572X-RAY DIFFRACTION100
3.5885-3.81330.29541420.20631595X-RAY DIFFRACTION100
3.8133-4.10760.27141410.20261576X-RAY DIFFRACTION100
4.1076-4.52070.24071460.17691608X-RAY DIFFRACTION100
4.5207-5.17420.20771450.16891612X-RAY DIFFRACTION100
5.1742-6.51670.24361460.20391645X-RAY DIFFRACTION100
6.5167-49.9160.25991540.18161721X-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)
11.10152.9070.60747.73252.35237.8643-0.39550.6973-0.482-0.4210.2221-1.03150.49361.10710.18010.63780.28710.2060.65740.04420.714354.857772.75850.1344
29.87810.6818-0.66032.4381-1.95782.71560.95172.1486-0.7322-1.464-0.389-0.17290.2646-0.1899-0.2650.97470.5984-0.1171.41360.04370.879953.781374.464643.1584
35.0263.18265.45154.60664.46426.3528-0.94520.3593-0.0291-0.78880.4582-0.203-0.79232.4001-0.1190.4382-0.0879-0.12861.28390.58411.366363.489587.755851.893
45.35642.33693.84016.23150.50726.838-0.71340.83410.7022-0.9902-0.089-0.4129-0.26161.17870.64650.45410.12960.16850.65090.07240.634948.574279.66648.5877
54.8947-0.31741.10282.4519-0.63586.6025-0.14731.39251.7119-0.0413-0.1394-0.6549-0.69720.3230.23170.4887-0.00590.05710.54330.25070.845146.441289.181845.6741
66.0406-1.41712.48624.6385-0.62861.9407-0.02640.50580.6222-0.1739-0.3775-0.56240.10360.41130.35240.39470.01160.06020.40020.06360.515139.081383.351752.3069
75.32053.70116.72593.4453.62719.51641.7356-2.6377-1.07152.024-0.6013-0.6232.8557-0.5599-1.11131.18790.0143-0.10811.3531-0.04390.708547.288770.405970.1635
84.28593.80392.09534.84034.64475.7350.3371-0.7128-0.331-0.68970.4839-0.6333-0.72910.3023-1.05590.51520.1370.11240.94470.03920.747852.325380.056866.5454
96.9607-4.24665.24854.4369-2.04554.9090.0816-0.050.1434-0.105-0.0881-0.18780.1429-0.06840.03390.4207-0.02240.08080.3451-0.0040.306729.725579.620749.6267
104.27980.0817-3.51590.1560.56625.5975-0.31810.628-0.6005-1.4337-0.18390.48860.3168-0.55610.4360.77370.0281-0.09050.5294-0.04150.372621.353273.540343.3159
112.60660.4160.08242.0434-1.76324.3229-0.52021.3448-0.33850.32841.3286-0.85471.90480.5332-0.7061.22410.2308-0.19290.8773-0.33310.71813.654576.380718.9134
122.71930.56481.35243.51563.16433.14260.46751.0766-0.2145-0.6744-0.25340.2288-0.164-0.1551-0.15730.88590.0829-0.05710.6802-0.01310.353413.493383.050322.4864
136.545-2.29841.43178.2361-4.48888.37270.45470.36510.0222-0.6037-0.46540.19190.25120.34060.08550.58790.0398-0.03730.3651-0.09990.381317.677784.687532.4928
144.1545-3.48220.3477.68743.49174.09610.37730.02261.7778-0.45330.1999-0.1958-0.5367-0.482-0.50480.49890.0582-0.14180.53550.05930.476415.895690.242733.5326
150.76840.47330.11082.5375-1.81292.7475-0.45320.23440.8462-0.1327-0.27010.5950.59750.12470.03130.94210.10580.18291.30020.05630.910926.072986.595116.0064
165.92360.4913-0.17976.39260.62486.4488-0.0910.4912-0.4906-0.1709-0.07720.09710.27120.50390.09870.53670.0936-0.07440.6869-0.08010.37254.910786.450922.7232
179.2075-2.24450.16843.8376-4.03334.83210.91860.14620.6468-0.28190.81791.525-0.9476-0.8737-1.82570.91720.2773-0.04140.8462-0.17890.81897.2208117.710759.1353
184.26933.1319-2.2224.8646-4.82344.99-0.1552-0.72861.66611.60041.57411.9167-1.0822-1.1987-1.49410.88840.17690.0460.7646-0.0121.32357.8657115.587166.4906
197.7168-2.13372.34048.2941-5.23394.83380.19620.74232.4435-0.2733-1.3928-0.4081-3.18020.38030.98951.4935-0.1771-0.3440.78250.20321.212121.8645126.769958.478
203.92962.9265-3.45557.4424-0.3464.06210.0638-0.61540.00750.5281-0.3860.7159-1.8030.65390.59040.81310.0433-0.18410.6199-0.0340.71114.268111.599260.7808
216.25823.7603-3.66125.4181-3.71743.50480.0841-0.81970.41130.273-0.5279-0.2265-0.95360.94220.33420.6649-0.1132-0.16590.59070.03120.788723.1931114.670663.8025
229.29580.42070.31763.6713-2.62246.53030.33090.31860.73950.2589-0.5228-1.67980.62860.69430.2161.23430.1458-0.1950.4189-0.03630.369924.969699.620866.1125
237.69940.94412.17219.32180.15228.68580.2928-0.4211-0.1531-0.311-0.5951-0.6772-0.98660.56050.40870.4017-0.0428-0.06610.5123-0.01090.626426.2187105.99454.5664
245.0364-2.1864-1.33473.8891-0.45748.9889-0.278-0.14520.4366-0.1936-0.02780.32910.13750.28170.23230.47870.0011-0.08230.4636-0.05210.588616.2006102.107654.5623
257.01052.6858-0.08336.0862-2.64251.3157-0.3333-0.9361-0.02790.1340.45250.2954-0.1113-1.0057-0.39970.4950.1426-0.02110.7562-0.08650.467115.371999.875462.585
263.37644.5976-3.30277.1747-2.91634.926-0.52620.97040.48680.05461.5965-0.14070.1025-0.6223-1.39270.93720.1037-0.14530.79270.19390.72376.7774111.13738.3102
272.2383-0.83270.94032.1108-1.43863.5986-0.2517-0.31640.44460.2190.18120.1054-0.5542-0.22670.09680.49340.0856-0.04470.4931-0.10630.45314.611796.876156.2431
284.2482.97420.47518.9806-1.1643.75580.54650.42791.76311.3401-1.22861.01941.03950.95410.29461.45780.75680.57552.42290.46841.27169.452383.699891.7735
297.57942.2438-0.8492.2546-1.79932.38111.20481.0398-0.73640.085-0.31890.77531.12450.3883-0.97710.6833-0.02280.09350.6966-0.01740.483515.625370.784488.5977
302.2395-0.5903-0.06864.0839-0.58356.2486-0.1214-0.529-0.08780.35880.1538-0.0031-0.0212-0.3118-0.05540.42130.07840.02230.68950.04920.396522.138877.028183.0698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 27 )
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 37 )
4X-RAY DIFFRACTION4chain 'A' and (resid 38 through 62 )
5X-RAY DIFFRACTION5chain 'A' and (resid 63 through 110 )
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 159 )
7X-RAY DIFFRACTION7chain 'A' and (resid 160 through 174 )
8X-RAY DIFFRACTION8chain 'B' and (resid 19 through 38 )
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 79 )
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 103 )
11X-RAY DIFFRACTION11chain 'B' and (resid 104 through 131 )
12X-RAY DIFFRACTION12chain 'B' and (resid 132 through 168 )
13X-RAY DIFFRACTION13chain 'B' and (resid 169 through 200 )
14X-RAY DIFFRACTION14chain 'B' and (resid 201 through 221 )
15X-RAY DIFFRACTION15chain 'B' and (resid 222 through 236 )
16X-RAY DIFFRACTION16chain 'B' and (resid 237 through 271 )
17X-RAY DIFFRACTION17chain 'C' and (resid 3 through 14 )
18X-RAY DIFFRACTION18chain 'C' and (resid 15 through 27 )
19X-RAY DIFFRACTION19chain 'C' and (resid 28 through 37 )
20X-RAY DIFFRACTION20chain 'C' and (resid 38 through 62 )
21X-RAY DIFFRACTION21chain 'C' and (resid 63 through 95 )
22X-RAY DIFFRACTION22chain 'C' and (resid 96 through 110 )
23X-RAY DIFFRACTION23chain 'C' and (resid 111 through 126 )
24X-RAY DIFFRACTION24chain 'C' and (resid 127 through 144 )
25X-RAY DIFFRACTION25chain 'C' and (resid 145 through 159 )
26X-RAY DIFFRACTION26chain 'C' and (resid 160 through 175 )
27X-RAY DIFFRACTION27chain 'D' and (resid 18 through 103 )
28X-RAY DIFFRACTION28chain 'D' and (resid 104 through 117 )
29X-RAY DIFFRACTION29chain 'D' and (resid 118 through 131 )
30X-RAY DIFFRACTION30chain 'D' and (resid 132 through 271 )

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