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- PDB-6i9i: Rift valley fever virus Gn in complex with a neutralizing antibod... -

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Basic information

Entry
Database: PDB / ID: 6i9i
TitleRift valley fever virus Gn in complex with a neutralizing antibody fragment
Components
  • Glycoprotein
  • RV-Gn1 Heavy chain
  • RV-Gn1 Light chain
KeywordsVIRAL PROTEIN / Glycoprotein / Antibody / phlebovirus / neutralization
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host apoptosis / 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
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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Rift valley fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsAllen, E.R. / Bowden, T.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N002091/1 United Kingdom
Medical Research Council (United Kingdom)MR/J007897/1 United Kingdom
CitationJournal: Cell Rep / Year: 2018
Title: A Protective Monoclonal Antibody Targets a Site of Vulnerability on the Surface of Rift Valley Fever Virus.
Authors: Allen, E.R. / Krumm, S.A. / Raghwani, J. / Halldorsson, S. / Elliott, A. / Graham, V.A. / Koudriakova, E. / Harlos, K. / Wright, D. / Warimwe, G.M. / Brennan, B. / Huiskonen, J.T. / Dowall, ...Authors: Allen, E.R. / Krumm, S.A. / Raghwani, J. / Halldorsson, S. / Elliott, A. / Graham, V.A. / Koudriakova, E. / Harlos, K. / Wright, D. / Warimwe, G.M. / Brennan, B. / Huiskonen, J.T. / Dowall, S.D. / Elliott, R.M. / Pybus, O.G. / Burton, D.R. / Hewson, R. / Doores, K.J. / Bowden, T.A.
History
DepositionNov 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_entity_id / _pdbx_entity_nonpoly.entity_id ..._atom_site.label_entity_id / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _struct_asym.entity_id / _struct_ref_seq.ref_id
Revision 2.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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: RV-Gn1 Heavy chain
B: RV-Gn1 Light chain
C: Glycoprotein
D: Glycoprotein
H: RV-Gn1 Heavy chain
L: RV-Gn1 Light chain


Theoretical massNumber of molelcules
Total (without water)165,0216
Polymers165,0216
Non-polymers00
Water7,963442
1
A: RV-Gn1 Heavy chain
B: RV-Gn1 Light chain
C: Glycoprotein


Theoretical massNumber of molelcules
Total (without water)82,5113
Polymers82,5113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-33 kcal/mol
Surface area21070 Å2
MethodPISA
2
D: Glycoprotein
H: RV-Gn1 Heavy chain
L: RV-Gn1 Light chain


Theoretical massNumber of molelcules
Total (without water)82,5113
Polymers82,5113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-35 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.590, 61.950, 78.910
Angle α, β, γ (deg.)81.01, 77.52, 84.74
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21H
12B
22L
13C
23D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPROPROAA1 - 2101 - 212
21THRTHRPROPROHE1 - 2101 - 212
12GLYGLYASPASPBB3 - 2102 - 215
22GLYGLYASPASPLF3 - 2102 - 215
13SERSERHISHISCC371 - 436218 - 283
23SERSERHISHISDD371 - 436218 - 283

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody RV-Gn1 Heavy chain


Mass: 23616.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody RV-Gn1 Light chain


Mass: 22819.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Protein Glycoprotein


Mass: 36075.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift valley fever virus / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: A2T080, UniProt: P21401*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O / References: UniProt: P21401*PLUS
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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG 500, 0.1 M bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.98→23.6 Å / Num. obs: 59882 / % possible obs: 96.2 % / Redundancy: 1.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.072 / Net I/σ(I): 5.8
Reflection shellResolution: 1.98→2.03 Å / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.67 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J02

4j02


Resolution: 1.98→23.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 14.777 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24343 3141 5 %RANDOM
Rwork0.20264 ---
obs0.20478 59882 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.972 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å2-0.77 Å20.97 Å2
2--1.74 Å20.28 Å2
3---0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.98→23.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7049 0 0 442 7491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.027229
X-RAY DIFFRACTIONr_bond_other_d0.0020.026320
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9449909
X-RAY DIFFRACTIONr_angle_other_deg0.897314774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7195946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07824.745255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.681151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.181518
X-RAY DIFFRACTIONr_chiral_restr0.0790.21170
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218079
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021383
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4713.353811
X-RAY DIFFRACTIONr_mcbond_other1.4713.3493810
X-RAY DIFFRACTIONr_mcangle_it2.4855.0064748
X-RAY DIFFRACTIONr_mcangle_other2.4855.0084749
X-RAY DIFFRACTIONr_scbond_it1.3993.4173418
X-RAY DIFFRACTIONr_scbond_other1.3953.4173418
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.265.0855162
X-RAY DIFFRACTIONr_long_range_B_refined5.02762.36728561
X-RAY DIFFRACTIONr_long_range_B_other4.92662.34828333
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A118920.08
12H118920.08
21B123020.1
22L123020.1
31C27600.1
32D27600.1
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 226 -
Rwork0.322 4318 -
obs--95.22 %
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)
10.18170.162-0.20440.4628-0.33261.1443-0.0656-0.08980.0797-0.03060.03180.0997-0.0184-0.19170.03380.03440.041-0.02720.33670.00480.113210.920246.508745.6234
20.46120.1575-0.3780.2759-0.30160.8376-0.1257-0.1162-0.0052-0.11870.00610.0730.19290.01590.11960.1562-0.02850.03150.22270.02620.134120.279131.131642.4061
32.62130.8973-0.33062.0140.0871.0636-0.01280.1809-0.0282-0.2090.0115-0.1109-0.2741-0.07870.00140.215-0.0394-0.01980.14140.09510.079630.693467.25920.0194
40.80770.90010.25172.3584-0.29840.34230.0816-0.0371-0.0780.165-0.0510.00340.00240.0211-0.03060.2123-0.02350.07870.12870.07010.0957-14.5917.641325.7803
50.5482-0.0793-0.39140.11960.09230.47480.09680.16470.06310.0739-0.1029-0.0337-0.0507-0.06450.00610.124-0.01010.01380.22640.09610.05710.729941.2912-0.5376
60.47070.0809-0.47120.4347-0.160.54840.02950.05120.00810.0619-0.0903-0.13960.01580.05780.06090.06680.01910.00310.2950.11990.077117.104234.34711.6136
70.2895-0.03550.03730.03140.05830.1547-0.00910.01370.03060.0037-0.00940.00370.0140.01220.01850.1626-0.03830.00220.18880.06310.085811.587838.210921.3342
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 210
2X-RAY DIFFRACTION2B2 - 211
3X-RAY DIFFRACTION3C371 - 439
4X-RAY DIFFRACTION4D370 - 437
5X-RAY DIFFRACTION5H1 - 211
6X-RAY DIFFRACTION6L3 - 211
7X-RAY DIFFRACTION7S1 - 442

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