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

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Basic information

Entry
Database: PDB / ID: 6egu
TitleStructure of RVFV envelope protein Gc in postfusion conformation in complex with 1,2-dipropionyl-sn-glycero-3-phosphocholine
ComponentsRVFV ENVELOPE PROTEIN GC
KeywordsVIRAL PROTEIN / viral fusion envelope glycoprotein bunyavirus phlebovirus
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
Chem-43Y / Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesRift Valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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 2.2Oct 23, 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: RVFV ENVELOPE PROTEIN GC
B: RVFV ENVELOPE PROTEIN GC
C: RVFV ENVELOPE PROTEIN GC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,90614
Polymers171,7333
Non-polymers3,17311
Water17,871992
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The oligomerization was also confirmed by SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18920 Å2
ΔGint-25 kcal/mol
Surface area51550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.567, 195.729, 65.496
Angle α, β, γ (deg.)90.00, 113.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RVFV ENVELOPE PROTEIN GC


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 / Plasmid: pT350 / Cell line (production host): S2 / 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.: 2
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.: 6 / 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-43Y / [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate / 1,2-dipropionyl-sn-glycero-3-phosphocholine


Mass: 370.356 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H29NO8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 992 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 14.1% (w/v) PEG 5000 MME, 0.1 M Bis-Tris pH 6.2, 0.1M (NH4)2SO4, 1.8 mM UDM, and 5% glycerol. Note: 80 mM 1,2-dipropionyl-sn-glycero-3-phosphocholine added to protein solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→39.15 Å / Num. obs: 65643 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.111 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.689 / Rpim(I) all: 0.429

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HJ1

4hj1


Resolution: 2.3→37.883 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 3306 5.04 %
Rwork0.1803 --
obs0.183 65591 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→37.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10086 0 199 992 11277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410527
X-RAY DIFFRACTIONf_angle_d0.75714196
X-RAY DIFFRACTIONf_dihedral_angle_d12.953852
X-RAY DIFFRACTIONf_chiral_restr0.0311630
X-RAY DIFFRACTIONf_plane_restr0.0031840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33290.29381420.22382578X-RAY DIFFRACTION100
2.3329-2.36770.28851520.23492606X-RAY DIFFRACTION100
2.3677-2.40470.31411350.24242554X-RAY DIFFRACTION100
2.4047-2.44410.28821310.24642601X-RAY DIFFRACTION100
2.4441-2.48620.31241330.23622590X-RAY DIFFRACTION100
2.4862-2.53140.31251400.2332608X-RAY DIFFRACTION100
2.5314-2.58010.30221360.23082590X-RAY DIFFRACTION100
2.5801-2.63280.29581250.22152589X-RAY DIFFRACTION100
2.6328-2.690.30681170.22212618X-RAY DIFFRACTION100
2.69-2.75250.30891210.22142582X-RAY DIFFRACTION100
2.7525-2.82140.29881260.21692627X-RAY DIFFRACTION100
2.8214-2.89760.26271500.20992548X-RAY DIFFRACTION100
2.8976-2.98290.28551260.20342616X-RAY DIFFRACTION100
2.9829-3.07910.23621450.18862611X-RAY DIFFRACTION100
3.0791-3.18910.22741420.18952548X-RAY DIFFRACTION100
3.1891-3.31670.24391590.17852584X-RAY DIFFRACTION100
3.3167-3.46760.20641400.1792601X-RAY DIFFRACTION100
3.4676-3.65020.21331320.16732611X-RAY DIFFRACTION100
3.6502-3.87870.22011370.15612591X-RAY DIFFRACTION100
3.8787-4.17780.1941670.13862573X-RAY DIFFRACTION100
4.1778-4.59760.1551450.12282608X-RAY DIFFRACTION100
4.5976-5.26140.1441370.11692587X-RAY DIFFRACTION100
5.2614-6.6230.191400.14572623X-RAY DIFFRACTION100
6.623-37.88830.19021280.16032641X-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)
10.3696-0.41230.01661.8911-0.60360.4499-0.0145-0.0009-0.1076-0.03410.03230.12670.1624-0.01410.01380.2011-0.01840.01370.2093-0.0050.205745.8036-74.686879.0481
20.4328-0.38140.00241.237-0.55980.5116-0.1033-0.1343-0.04630.17620.09370.00040.00530.04470.00050.20730.00490.00490.22970.01140.182151.5739-65.243799.3173
30.2762-0.6024-0.0511.7537-0.32750.27110.02190.0454-0.0477-0.0376-0.1504-0.20310.09960.0986-0.00780.15740.01950.02440.25920.03990.246467.5685-68.511482.2705
4-0.0611-0.6556-0.01612.1044-0.89240.4989-0.01660.04660.04850.02570.02610.0642-0.1112-0.07530.00030.1943-0.0109-0.05380.20810.01070.224630.6773-25.090560.8805
50.2165-0.20430.20491.9042-0.31370.5211-0.0605-0.04610.13870.13370.05890.1217-0.2349-0.0304-0.00030.2787-0.0023-0.01950.192-0.02530.207341.886-14.326281.4035
60.2178-0.1254-0.02771.3826-0.29890.48510.00830.07990.1267-0.0437-0.1091-0.2155-0.09630.0722-0.02160.1711-0.02090.02710.20230.05480.232255.7795-19.217760.2681
70.2005-0.0830.03790.9752-0.26920.89950.04260.0437-0.0091-0.3249-0.03380.00240.31430.1465-0.00440.27830.02420.05150.23140.00370.162461.4701-64.712760.2115
80.8792-0.2772-0.07320.92660.17440.4131-0.0558-0.1586-0.30160.15740.21840.5590.105-0.19190.14440.16490.00390.03480.26860.11380.310528.506-62.503387.4788
90.0401-0.530.15653.5971-1.06710.3626-0.12420.00020.13921.677-0.5352-1.7956-0.28210.1967-2.7910.4926-0.0327-0.39520.30820.08510.552166.7361-48.0865100.1276
100.5318-0.59130.47951.4095-0.5350.65940.17970.31920.5341-0.521-0.2532-0.3955-0.0547-0.0433-0.04580.27520.0507-0.01150.20880.06660.23238.7523-26.342452.8954
110.2219-0.5622-0.13813.23831.06970.3754-0.0564-0.11370.0144-0.4090.06470.8731-0.3759-0.32220.13380.38340.0506-0.03320.1874-0.01750.26731.0486-19.228579.3041
120.36950.2106-0.37540.1335-0.40791.40680.00650.03060.13660.3108-0.0035-0.3072-0.57910.03840.07990.2948-0.0727-0.04530.18790.01890.320458.4558-14.714270.3505
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 1117:1135)))

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