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- PDB-4zxs: HSV-1 nuclear egress complex -

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Basic information

Entry
Database: PDB / ID: 4zxs
TitleHSV-1 nuclear egress complex
Components(Virion egress protein ...) x 2
KeywordsVIRAL PROTEIN / HSV-1 / nuclear egress / UL31 / UL34 / membrane deformation
Function / homology
Function and homology information


exit of virus from host cell nucleus by nuclear egress / viral budding from nuclear membrane / host cell nuclear inner membrane / 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
NICKEL (II) ION / Nuclear egress protein 1 / Nuclear egress protein 2
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.772 Å
AuthorsBigalke, J.M. / Heldwein, E.E.
Funding support Germany, United States, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)BI 1658/1-1 Germany
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM111795-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI097573-01A1 United States
Burroughs Wellcome Fund United States
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
DepositionMay 20, 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 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,93913
Polymers97,5384
Non-polymers4019
Water1,33374
1
A: Virion egress protein UL34
B: Virion egress protein UL31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9877
Polymers48,7692
Non-polymers2185
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Virion egress protein UL34
D: Virion egress protein UL31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9526
Polymers48,7692
Non-polymers1834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Virion egress protein UL34
B: Virion egress protein UL31
C: Virion egress protein UL34
D: Virion egress protein UL31
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)587,63178
Polymers585,22824
Non-polymers2,40354
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
crystal symmetry operation4_755-x+2,-y,z1
crystal symmetry operation5_665y+1,-x+y+1,z1
crystal symmetry operation6_545x-y,x-1,z1
Buried area72490 Å2
ΔGint-745 kcal/mol
Surface area196020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.529, 110.529, 155.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

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Virion egress protein ... , 2 types, 4 molecules ACBD

#1: Protein Virion egress protein UL34 / Primary envelopment factor UL34


Mass: 20081.971 Da / Num. of mol.: 2 / Fragment: UNP residues 15-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Strain: 17 / Gene: UL34 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P10218
#2: Protein Virion egress protein UL31


Mass: 28687.035 Da / Num. of mol.: 2 / Fragment: UNP residues 51-306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Strain: 17 / Gene: UL31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P10215

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Non-polymers , 5 types, 83 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Na citrate pH 5.6, 5 mM NiCl2, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.6 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 2.772→47.86 Å / Num. obs: 27365 / % possible obs: 99.78 % / Redundancy: 19 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 34.37
Reflection shellResolution: 2.772→2.87 Å / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 4.57 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z3U

4z3u


Resolution: 2.772→47.86 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 27.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 1368 5 %
Rwork0.217 --
obs0.2195 27361 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.772→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6236 0 9 74 6319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036397
X-RAY DIFFRACTIONf_angle_d0.758685
X-RAY DIFFRACTIONf_dihedral_angle_d12.6422322
X-RAY DIFFRACTIONf_chiral_restr0.029957
X-RAY DIFFRACTIONf_plane_restr0.0041132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7717-2.87080.35341320.27162530X-RAY DIFFRACTION98
2.8708-2.98570.35351380.26392603X-RAY DIFFRACTION100
2.9857-3.12160.31471360.23642591X-RAY DIFFRACTION100
3.1216-3.28610.31591360.23312592X-RAY DIFFRACTION100
3.2861-3.49190.27341370.2292588X-RAY DIFFRACTION100
3.4919-3.76150.29561360.22512597X-RAY DIFFRACTION100
3.7615-4.13980.22191380.20572608X-RAY DIFFRACTION100
4.1398-4.73840.24161370.19092611X-RAY DIFFRACTION100
4.7384-5.9680.2671370.20732609X-RAY DIFFRACTION100
5.968-47.86760.22391410.21412664X-RAY DIFFRACTION100
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)
17.53645.75173.54394.82971.21767.2225-0.18610.9422.6603-1.977-0.9482.5244-1.0456-2.5985-0.54821.16230.52440.11710.46470.58250.56361.83160.9733-64.7983
28.2894-1.1446-7.1293.4841.47556.75551.0286-0.64380.5638-0.58541.04020.0742-3.47780.5537-1.39250.86690.204-0.13720.71320.19910.446167.42364.9048-59.7849
33.62030.13730.89881.8588-1.27268.55650.40640.1803-0.0402-0.3329-0.43590.2081-0.7152-0.3653-0.14430.52510.1270.02960.3284-0.03240.294470.5088-2.9731-56.5223
43.7749-0.15950.32773.16571.55641.7441-0.1134-0.25911.27980.3053-0.10220.17610.98321.211-0.40040.73450.23340.34840.8963-0.05510.183382.5916-5.6164-54.9004
54.0416-2.1855-1.68226.08944.35368.5680.340.08240.1441-0.3905-0.0049-0.15720.0380.5602-0.12740.3720.08590.03490.3450.11030.340774.6223-13.2447-54.6522
62.2243-1.0098-0.38871.888-0.71664.86940.34610.5922-0-0.6783-0.25650.25830.12780.0265-0.0750.53930.0516-0.07610.4049-0.00940.324771.6394-20.1616-54.606
73.2735-2.9315-1.16817.6873-0.27147.92720.3617-0.13030.10010.2662-0.37420.45710.711-0.23160.05580.4642-0.08840.04510.4109-0.02830.263372.2461-29.3881-17.8558
81.65410.2529-1.04863.5591-0.86088.12630.0506-0.29140.19310.20670.006-0.23820.52440.1169-0.05280.39450.0114-0.02550.3767-0.05960.247779.4998-28.6364-24.0964
96.49171.73991.26965.84732.07835.8020.98590.4803-1.5075-0.3783-0.1423-0.3484-0.17842.0196-0.38950.63540.239-0.04010.7195-0.11250.4774102.2543-47.749957.8356
100.7516-0.72930.09240.8875-0.94435.5837-0.2808-2.75051.01861.0942-0.6173-2.01540.2421.92661.34090.8657-0.077-0.19731.7605-0.16430.8722112.2006-39.226862.1906
113.2119-0.1032-0.50253.7865-1.12831.7716-0.1246-0.7284-0.3161-0.02470.5573-0.04730.17381.0037-0.11830.42820.1727-0.0920.8850.01570.418699.7014-38.746254.7701
124.64031.40273.21231.793-0.12063.0709-0.1009-0.2479-0.0970.33070.2352-0.4446-1.22150.30110.0050.62870.0749-0.03140.56330.00260.38499.9185-30.714148.4528
134.6218-0.105-1.5817.42791.38163.8309-0.1032-0.6510.16130.60110.15740.2718-0.69950.30880.59690.58270.1107-0.02620.54230.03990.34489.1216-33.003854.1141
142.179-0.91151.02382.6531-1.05912.49990.0625-0.2141-0.2220.45850.24810.0836-0.14940.21050.19060.49130.063-0.01560.7745-0.0410.379585.5431-33.386654.5795
158.4041-1.1629-5.26912.19052.78755.41580.0292-0.45470.6107-0.4423-0.73610.39040.444-1.13090.57870.70750.02330.06060.68720.12090.422273.5063-38.22440.0122
163.6631-2.56041.8055.19880.76153.47210.1993-0.0064-0.1416-0.1864-0.15630.10990.6468-0.2909-0.17820.6224-0.07740.04280.5390.02090.348175.129-32.474415.1481
174.53681.8213-1.71023.91220.01573.0934-0.20640.97770.1241-0.30020.2209-0.0599-0.624-0.9546-0.26480.5534-0.0111-0.0390.4376-0.00230.366577.7184-23.550623.8895
181.9207-0.47961.59952.82230.75913.6868-0.08020.27880.0976-0.40020.1471-0.185-0.4420.1077-0.22190.53890.00250.07220.59990.03490.243376.7069-26.009620.4501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 99 )
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 116 )
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 172 )
6X-RAY DIFFRACTION6chain 'B' and (resid 55 through 136 )
7X-RAY DIFFRACTION7chain 'B' and (resid 137 through 200 )
8X-RAY DIFFRACTION8chain 'B' and (resid 201 through 306 )
9X-RAY DIFFRACTION9chain 'C' and (resid 14 through 39 )
10X-RAY DIFFRACTION10chain 'C' and (resid 40 through 51 )
11X-RAY DIFFRACTION11chain 'C' and (resid 52 through 92 )
12X-RAY DIFFRACTION12chain 'C' and (resid 93 through 124 )
13X-RAY DIFFRACTION13chain 'C' and (resid 125 through 175 )
14X-RAY DIFFRACTION14chain 'D' and (resid 55 through 118 )
15X-RAY DIFFRACTION15chain 'D' and (resid 119 through 136 )
16X-RAY DIFFRACTION16chain 'D' and (resid 137 through 200 )
17X-RAY DIFFRACTION17chain 'D' and (resid 201 through 227 )
18X-RAY DIFFRACTION18chain 'D' and (resid 228 through 306 )

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