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- PDB-6egt: Structure of RVFV envelope protein Gc in postfusion conformation ... -

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Basic information

Entry
Database: PDB / ID: 6egt
TitleStructure of RVFV envelope protein Gc in postfusion conformation in complex with MES
ComponentsGlycoprotein
KeywordsVIRAL PROTEIN / fusion protein viral envelope lipid interaction viral fusion
Function / homology
Function and homology information


host cell mitochondrial outer membrane / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Immunoglobulin-like - #3770 / Phlebovirus nonstructural NS-M / M polyprotein precursor, phlebovirus / Phlebovirus nonstructural protein NS-M / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain ...Immunoglobulin-like - #3770 / Phlebovirus nonstructural NS-M / M polyprotein precursor, phlebovirus / Phlebovirus nonstructural protein NS-M / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesRift valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGuardado-Calvo, P. / Rey, F.A.
CitationJournal: Science / Year: 2017
Title: A glycerophospholipid-specific pocket in the RVFV class II fusion protein drives target membrane insertion.
Authors: Guardado-Calvo, P. / Atkovska, K. / Jeffers, S.A. / Grau, N. / Backovic, M. / Perez-Vargas, J. / de Boer, S.M. / Tortorici, M.A. / Pehau-Arnaudet, G. / Lepault, J. / England, P. / Rottier, P. ...Authors: Guardado-Calvo, P. / Atkovska, K. / Jeffers, S.A. / Grau, N. / Backovic, M. / Perez-Vargas, J. / de Boer, S.M. / Tortorici, M.A. / Pehau-Arnaudet, G. / Lepault, J. / England, P. / Rottier, P.J. / Bosch, B.J. / Hub, J.S. / Rey, F.A.
History
DepositionSep 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 6, 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
B: Glycoprotein
C: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,26114
Polymers171,7333
Non-polymers2,52711
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The oligomerization state was checked by SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18510 Å2
ΔGint-16 kcal/mol
Surface area53790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.306, 102.030, 198.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Glycoprotein


Mass: 57244.469 Da / Num. of mol.: 3 / Mutation: W821H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift valley fever virus / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A2T087, UniProt: P03518*PLUS
#2: Polysaccharide beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}}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.: 8 / Source method: obtained synthetically / 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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 12%(w/v) PEG 5000 MME, 0.1M MES 6.2, 0.1M (NH4)SO4, 1.8 mM UDM, 5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.5→38.44 Å / Num. obs: 51348 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.58 Å / Rmerge(I) obs: 0.735 / Rpim(I) all: 0.541

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1471refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HJ1

4hj1


Resolution: 2.5→29.497 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.55
RfactorNum. reflection% reflection
Rfree0.2351 2036 3.97 %
Rwork0.1955 --
obs0.1971 51275 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10127 0 160 287 10574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410525
X-RAY DIFFRACTIONf_angle_d0.9214188
X-RAY DIFFRACTIONf_dihedral_angle_d14.1633796
X-RAY DIFFRACTIONf_chiral_restr0.0351616
X-RAY DIFFRACTIONf_plane_restr0.0041840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.61380.31841240.28326159X-RAY DIFFRACTION99
2.6138-2.75150.30693650.26795944X-RAY DIFFRACTION99
2.7515-2.92380.29732460.24856145X-RAY DIFFRACTION100
2.9238-3.14930.30191990.22986184X-RAY DIFFRACTION100
3.1493-3.46580.24293060.21136103X-RAY DIFFRACTION100
3.4658-3.96620.21762550.17956170X-RAY DIFFRACTION99
3.9662-4.99310.18152670.14196165X-RAY DIFFRACTION99
4.9931-29.4990.19342740.15426369X-RAY DIFFRACTION98
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)
10.4177-0.2261-0.58890.24240.52122.71360.02940.0605-0.0294-0.1016-0.0177-0.01090.1370.05330.01030.2404-0.0051-0.02640.2419-0.00780.227118.776318.483519.0622
21.2317-0.129-0.99520.41150.12131.91030.0528-0.06-0.0337-0.0634-0.0188-0.0330.18810.30260.01250.22270.07220.00120.2467-0.0250.25139.862414.616128.0961
30.3103-0.1362-0.16050.17-0.21891.74070.07920.07060.0368-0.1511-0.0378-0.0776-0.20860.1336-0.00020.21770.00310.0270.2347-0.00630.260433.036136.629423.571
40.51380.005-0.93970.0883-0.01851.7499-0.0066-0.0173-0.00030.06310.04390.0130.0464-0.09490.00010.2011-0.02750.00630.21620.01660.2024-2.452420.074470.2193
50.71630.1288-0.45150.54690.17872.16720.0333-0.2399-0.01240.1454-0.0097-0.0383-0.02230.11370.00020.2260.0117-0.02940.28470.00270.21321.533919.927979.8124
60.6185-0.0465-0.74470.4534-0.16432.06940.1267-0.04320.08820.1164-0.00210.0615-0.1631-0.11620.00160.2226-0.02860.03170.1785-0.02340.224410.238342.371573.3656
70.7677-0.6587-0.17220.6076-0.03390.79980.07750.10970.1362-0.10980.0162-0.011-0.0093-0.34170.00050.26610.04230.03570.2446-0.00480.253211.188942.918627.5923
80.50240.3869-0.52341.36390.07040.7747-0.00460.0938-0.0757-0.12310.03910.16560.15840.00430.00090.29170.0145-0.00650.2329-0.01540.214817.72070.365433.6196
90.9592-0.14920.32360.57060.04970.9630.14040.0929-0.0039-0.0363-0.0379-0.14930.07950.3771-0.00030.22850.03760.0070.413-0.03010.258748.937728.944243.9501
100.61390.02850.41080.60610.35040.45710.2495-0.16030.15880.0108-0.05240.1187-0.19120.07410.00670.21770.0365-0.0090.2378-0.0150.2875-5.08931.092867.9328
110.57920.04160.3470.97040.42375.04850.1954-0.08270.07890.2404-0.18160.05150.4531-0.568-0.05420.2112-0.0449-0.03240.1189-0.01740.277214.010411.426177.1179
120.38390.44870.0420.6143-0.10450.2705-0.2053-0.4432-0.04670.07220.2182-0.04250.12090.4528-0.00110.25950.0012-0.04860.38490.03110.19621.451939.134676.7701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and ((resseq 691:758))) or (chain 'A' and ((resseq 852:900))) or (chain 'A' and ((resseq 981:1023)))
2X-RAY DIFFRACTION2(chain 'B' and ((resseq 691:758))) or (chain 'B' and ((resseq 852:900))) or (chain 'B' and ((resseq 981:1023)))
3X-RAY DIFFRACTION3(chain 'C' and ((resseq 691:758))) or (chain 'C' and ((resseq 852:900))) or (chain 'C' and ((resseq 981:1023)))
4X-RAY DIFFRACTION4(chain 'A' and ((resseq 759:851))) or (chain 'A' and ((resseq 901:980)))
5X-RAY DIFFRACTION5(chain 'B' and ((resseq 759:851))) or (chain 'B' and ((resseq 901:980)))
6X-RAY DIFFRACTION6(chain 'C' and ((resseq 759:851))) or (chain 'C' and ((resseq 901:980)))
7X-RAY DIFFRACTION7(chain 'A' and ((resseq 1024:1116)))
8X-RAY DIFFRACTION8(chain 'B' and ((resseq 1024:1116)))
9X-RAY DIFFRACTION9(chain 'C' and ((resseq 1024:1116)))
10X-RAY DIFFRACTION10(chain 'A' and ((resseq 1117:1135)))
11X-RAY DIFFRACTION11(chain 'B' and ((resseq 1117:1135)))
12X-RAY DIFFRACTION12(chain 'C' and ((resseq 1117:1134)))

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