[English] 日本語
Yorodumi
- PDB-5i2s: PREFUSION FORM OF THE VESICULAR STOMATITIS VIRUS GLYCOPROTEIN G E... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i2s
TitlePREFUSION FORM OF THE VESICULAR STOMATITIS VIRUS GLYCOPROTEIN G ECTODOMAIN
ComponentsGlycoprotein G
KeywordsVIRAL PROTEIN / VIRION PROTEIN / MEMBRANE PROTEIN / ENVELOPE PROTEIN / MEMBRANE FUSION
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
PH-domain like - #130 / Rhabdovirus spike glycoprotein G, lateral domain / Helix Hairpins - #740 / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / Helix Hairpins / PH-domain like / Helix non-globular / Special / SH3 type barrels. ...PH-domain like - #130 / Rhabdovirus spike glycoprotein G, lateral domain / Helix Hairpins - #740 / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / Helix Hairpins / PH-domain like / Helix non-globular / Special / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
YTTERBIUM (III) ION / Glycoprotein G
Similarity search - Component
Biological speciesVesicular stomatitis Indiana virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRoche, S. / Bressanelli, S.
CitationJournal: Science / Year: 2007
Title: Structure of the prefusion form of the vesicular stomatitis virus glycoprotein G.
Authors: Roche, S. / Rey, F.A. / Gaudin, Y. / Bressanelli, S.
History
DepositionFeb 9, 2016Deposition site: RCSB / Processing site: PDBE
SupersessionMar 2, 2016ID: 2J6J, 2j6j
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3345
Polymers47,3421
Non-polymers9924
Water00
1
A: Glycoprotein G
hetero molecules

A: Glycoprotein G
hetero molecules

A: Glycoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,00115
Polymers142,0263
Non-polymers2,97512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6510 Å2
ΔGint-26 kcal/mol
Surface area55900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.510, 120.510, 183.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-504-

YB

21A-505-

YB

-
Components

#1: Protein Glycoprotein G


Mass: 47342.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Vesicular stomatitis Indiana virus (strain Mudd-Summers)
Strain: Mudd-Summers / References: UniProt: P0C2X0
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Yb

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 0.1M TRIS PH 8.7, NANO3 0.4M, PEG 4000 24%

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.3861 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3861 Å / Relative weight: 1
ReflectionResolution: 3→45 Å / Num. obs: 16104 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.6
Reflection shellResolution: 3→3.2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.7 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CMZ

2cmz
PDB Unreleased entry


Resolution: 3→14.942 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / Phase error: 21.78
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 816 5.07 %Random
Rwork0.1813 ---
obs0.1841 16104 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→14.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 44 0 3308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063415
X-RAY DIFFRACTIONf_angle_d0.9074659
X-RAY DIFFRACTIONf_dihedral_angle_d13.6752002
X-RAY DIFFRACTIONf_chiral_restr0.054501
X-RAY DIFFRACTIONf_plane_restr0.005592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0004-3.18670.34981520.28542419X-RAY DIFFRACTION98
3.1867-3.430.34261290.24882483X-RAY DIFFRACTION99
3.43-3.77010.29211370.21172518X-RAY DIFFRACTION100
3.7701-4.30420.22541400.16262546X-RAY DIFFRACTION100
4.3042-5.38040.17441290.14262583X-RAY DIFFRACTION100
5.3804-14.94210.18491290.15032739X-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)
15.72560.8447-0.21742.4597-1.15611.4652-0.2028-0.0829-0.857-0.16760.1054-0.40840.2270.18110.10780.32480.02660.09020.29610.00980.5534.563545.022658.964
24.55461.3851-1.50583.0111-0.28713.94210.276-0.4344-0.00880.1125-0.18510.04320.03560.1388-0.07240.3311-0.02560.03830.53350.10140.3337-13.77946.545683.553
34.441.05870.26442.87191.21778.0215-0.02950.2286-0.4489-0.3140.0328-0.28930.2209-0.1880.03860.3112-0.05490.12350.3702-0.07830.4963-18.567241.586453.7956
42.35040.1808-0.47491.11550.59280.59650.52231.47340.0801-1.8096-0.42310.52610.4907-0.72830.01271.4831-0.00820.12621.4989-0.14840.6717-21.073941.883126.4262
52.7686-0.0925-1.50933.8450.80373.6098-0.21140.3527-0.2844-0.2438-0.15610.5161-0.1654-0.08690.37420.24770.00730.00780.3405-0.02010.3733-4.075759.643954.7408
63.03853.26953.78464.26655.12446.19760.55580.09-1.21730.05690.24570.07540.24250.676-0.83020.99180.17770.15610.5536-0.06710.8229-10.698334.414167.5236
70.00760.00150.00450.00030.00430.02210.6658-0.2824-0.36180.41080.25910.02490.6835-0.1969-0.80581.3428-0.15090.09860.6708-0.08721.3457-18.384829.392570.4986
81.4727-0.418-0.60190.9823-1.3563.0484-0.15920.09820.07510.12310.24970.4234-0.32540.0468-0.1410.41790.0935-0.02640.37070.04640.427-12.513454.904670.0653
94.9888-2.512-0.48026.2177-2.06769.63480.3594-0.88941.03950.7051-0.4669-0.78150.03860.52050.02670.4909-0.1044-0.02060.5765-0.09950.4411-3.174558.592975.3435
107.17381.91012.04313.79321.49244.9513-0.17820.8398-0.3651-0.54850.2415-0.22690.21820.4289-0.05530.33210.03890.00960.402-0.01840.35118.805356.853752.262
111.01540.1891-2.71280.0355-0.51037.3511-0.5334-0.05350.0441-0.38610.2201-0.1376-0.4086-0.43190.32651.3921-0.0455-0.23771.4725-0.15210.9331-11.560647.083436.3062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:17) or (chain A and resseq 310:382) or (chain A and resseq 1416:1416)
2X-RAY DIFFRACTION2(chain A and resseq 36:46) or (chain A and resseq 181:258) or (chain A and resseq 1418:1418)
3X-RAY DIFFRACTION3(chain A and resseq 53:59) or (chain A and resseq 130:172) or (chain A and resseq 1414:1415)
4X-RAY DIFFRACTION4(chain A and resseq 60:129)
5X-RAY DIFFRACTION5(chain A and resseq 18:25) or (chain A and resseq 274:309) or (chain A and resseq 1417:1417)
6X-RAY DIFFRACTION6(chain A and resseq 47:52)
7X-RAY DIFFRACTION7(chain A and resseq 173:180)
8X-RAY DIFFRACTION8(chain A and resseq 259:273)
9X-RAY DIFFRACTION9(chain A and resseq 26:35)
10X-RAY DIFFRACTION10(chain A and resseq 383:405)
11X-RAY DIFFRACTION11(chain A and resseq 406:413)

+
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