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- PDB-5i2s: PREFUSION FORM OF THE VESICULAR STOMATITIS VIRUS GLYCOPROTEIN G E... -

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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
Revision 2.2Oct 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: 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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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%

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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

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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)

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