[English] 日本語
Yorodumi
- PDB-4zxs: HSV-1 nuclear egress complex -

+
Open data


ID or keywords:

Loading...

-
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 / host cell nuclear inner membrane / viral budding from nuclear membrane / membrane / metal ion binding
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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

Read more