[English] 日本語
Yorodumi
- PDB-8ini: vaccinia H2 protein without the transmembrane region -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ini
Titlevaccinia H2 protein without the transmembrane region
Componentsvaccinia h2 protein
KeywordsVIRAL PROTEIN / membrane fusion / entry component
Function / homologyViral late protein H2 / Viral late protein H2 / membrane fusion involved in viral entry into host cell / symbiont entry into host cell / virion membrane / membrane / H2
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLiu, C.Y. / Ko, T.P. / Wang, H.C. / Chang, W.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: J.Virol. / Year: 2023
Title: Structural and functional analyses of viral H2 protein of the vaccinia virus entry fusion complex.
Authors: Kao, C.F. / Liu, C.Y. / Hsieh, C.L. / Carillo, K.J.D. / Tzou, D.L.M. / Wang, H.C. / Chang, W.
History
DepositionMar 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.page_first ..._audit_author.name / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 3, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: vaccinia h2 protein
B: vaccinia h2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8043
Polymers22,6102
Non-polymers1941
Water4,990277
1
A: vaccinia h2 protein


Theoretical massNumber of molelcules
Total (without water)11,3051
Polymers11,3051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: vaccinia h2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4992
Polymers11,3051
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.735, 60.416, 131.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-300-

PG4

21A-312-

HOH

31A-318-

HOH

41A-320-

HOH

51B-485-

HOH

61B-501-

HOH

71B-503-

HOH

81B-526-

HOH

91B-528-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPPROPRO(chain 'A' and (resid 9 through 56 or resid 58...AA9 - 565 - 52
12ALAALACYSCYS(chain 'A' and (resid 9 through 56 or resid 58...AA58 - 6254 - 58
13TYRTYRLYSLYS(chain 'A' and (resid 9 through 56 or resid 58...AA64 - 6960 - 65
14ASNASNMETMET(chain 'A' and (resid 9 through 56 or resid 58...AA71 - 9167 - 87
15PROPROASNASN(chain 'A' and (resid 9 through 56 or resid 58...AA93 - 10189 - 97
26ASPASPPROPRO(chain 'B' and (resid 9 through 56 or resid 58...BB9 - 565 - 52
27ALAALACYSCYS(chain 'B' and (resid 9 through 56 or resid 58...BB58 - 6254 - 58
28TYRTYRLYSLYS(chain 'B' and (resid 9 through 56 or resid 58...BB64 - 6960 - 65
29ASNASNMETMET(chain 'B' and (resid 9 through 56 or resid 58...BB71 - 9167 - 87
210PROPROASNASN(chain 'B' and (resid 9 through 56 or resid 58...BB93 - 10189 - 97

-
Components

#1: Protein vaccinia h2 protein


Mass: 11304.950 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: VACV_BRZ_SERRO2_098 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q1PIU9
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium Chloride, Bicine, PEG 550 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 19019 / % possible obs: 98.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.02 / Net I/σ(I): 34.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1895 / CC1/2: 0.915 / Rpim(I) all: 0.26 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→19.84 Å / SU ML: 0.1773 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2037 895 5 %
Rwork0.1694 17003 -
obs0.1712 17898 93.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.76 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 13 277 1808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751576
X-RAY DIFFRACTIONf_angle_d1.0122114
X-RAY DIFFRACTIONf_chiral_restr0.0645210
X-RAY DIFFRACTIONf_plane_restr0.0066271
X-RAY DIFFRACTIONf_dihedral_angle_d14.4824579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.860.24321160.1952198X-RAY DIFFRACTION73.62
1.86-20.24291450.17762753X-RAY DIFFRACTION91.16
2-2.20.22271560.17562973X-RAY DIFFRACTION99.43
2.2-2.520.2341600.17583025X-RAY DIFFRACTION99.53
2.52-3.180.1971580.18393014X-RAY DIFFRACTION98.48
3.18-19.840.17881600.15273040X-RAY DIFFRACTION96.1
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)
10.403094991206-0.1376246805180.2263702579560.044099175638-0.04877748162250.209711673042-0.0003175256903780.133857861473-0.05609944543430.0428076901491-0.0670500579438-0.1293171721720.1708292729610.120301534448-0.05359086235140.1931537244810.0104743550284-0.005464701565410.0833929458890.02676363026890.20098649837816.2530694392-12.1269037017-7.79184293537
20.435434041117-0.0462196945711-0.4020802333260.486019652722-0.1580205631010.4468706966610.0149146514934-0.1551758642580.03233848624220.208357046296-0.0163251597357-0.00894432115733-0.0840598501286-0.06388402811850.002687857664220.179889957952-0.005593554572260.01134766504830.08738024451380.04199430540840.19838487324712.1553531708-7.981538853610.130030946449
30.405726959545-0.08808608239810.4219819660860.445578413713-0.03022269596780.403672530645-0.006963280487060.200457265768-0.08167237769970.0294313718914-0.0673991310712-0.00313050219822-0.06080458263160.05564187178840.0004415573003550.192781399223-0.000631768228088-0.01224907407170.129492679497-0.006328081587790.1527576646778.67275390483-9.84669998248-15.6337741638
40.7456728370160.4153850112530.3193693023420.670771159041-0.4000720732180.7734411038280.0815278088913-0.177581794839-0.0573545501510.421302584380.000218561917145-0.18374423315-0.1589652672740.08471243717050.05146971947540.231075186872-0.01054838755220.01265687715140.09254858594060.04248144944930.16054101592910.5596159532-14.25940091594.49945329837
50.3462478020260.218816701114-0.5598879731970.4398656089380.09526778287531.59091222362-0.079069034943-0.455998838978-0.2296558993480.1382010155860.120398190907-0.028395761307-0.0532278778430.197735313030.03512935944560.1475709738060.0941732065230.04204581725880.2465994860580.1156511505620.283095576128-4.0479331619-11.528356950924.5905619116
60.3505399181470.103726470267-0.07965898918810.1598669175690.06062198892530.074937057126-0.157194038339-0.0248491515534-0.113461454506-0.2792981493810.0572300969798-0.1485714033640.141151827177-0.403030651666-6.46278811004E-50.139074518577-0.01690398205520.006056169194780.219869416312-0.004728185422430.170248776627-8.84115650674-2.1735619794719.073760641
72.278673488541.17795451274-0.7272565362583.0408426115-0.4689650429760.67138512052-0.123781656966-0.919436567227-0.0200077925979-0.007001005108720.0622111868623-0.03738127818830.04380615670590.0518115279811-0.2416879688610.0928747661194-0.00823952313440.01491029449760.337449557010.05217775612620.0596031622345-7.55678742662-2.1445872416830.6432946261
80.4152333280450.330752645308-0.1961647226390.50260437169-0.2044001370030.658265753671-0.1425035399880.05937658344-0.00727491722918-0.1985035450990.08899715278110.106155628929-0.1393366740150.235046572534-0.01018314479730.157380113505-0.001794797957010.011253579660.2163070755710.006089870614320.138322364799-2.759851558852.8600230648415.4837337798
90.368722054119-0.21591680817-0.5593356164830.4883313307360.3023193440820.9179491445530.00357182463156-0.5700200808760.0802457187029-0.152389928917-0.09417507663380.1175786103740.111704462726-0.0431967076493-0.01171417831150.06016928483330.03226538032266.55700622212E-50.350506692757-0.0388572577080.139926815822-13.81558622661.9175963612629.2929581013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 103 )
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 14 )
6X-RAY DIFFRACTION6chain 'B' and (resid 15 through 28 )
7X-RAY DIFFRACTION7chain 'B' and (resid 29 through 43 )
8X-RAY DIFFRACTION8chain 'B' and (resid 44 through 68 )
9X-RAY DIFFRACTION9chain 'B' and (resid 69 through 101 )

+
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://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