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- PDB-6iek: Structure of RVFV Gn and human monoclonal antibody R12 -

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Basic information

Entry
Database: PDB / ID: 6iek
TitleStructure of RVFV Gn and human monoclonal antibody R12
Components
  • Heavy chain of Fab R12
  • Light chain of Fab R12
  • NSmGnGc
KeywordsSTRUCTURAL PROTEIN/IMMUNE SYSTEM / RVFV / antibody / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-IMMUNE SYSTEM complex
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 / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / 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 speciesRift valley fever virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsWang, Q.H. / Wu, Y. / Gao, F. / Qi, J.X. / Gao, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31390432 China
CitationJournal: Nat Microbiol / Year: 2019
Title: Neutralization mechanism of human monoclonal antibodies against Rift Valley fever virus.
Authors: Wang, Q. / Ma, T. / Wu, Y. / Chen, Z. / Zeng, H. / Tong, Z. / Gao, F. / Qi, J. / Zhao, Z. / Chai, Y. / Yang, H. / Wong, G. / Bi, Y. / Wu, L. / Shi, R. / Yang, M. / Song, J. / Jiang, H. / An, ...Authors: Wang, Q. / Ma, T. / Wu, Y. / Chen, Z. / Zeng, H. / Tong, Z. / Gao, F. / Qi, J. / Zhao, Z. / Chai, Y. / Yang, H. / Wong, G. / Bi, Y. / Wu, L. / Shi, R. / Yang, M. / Song, J. / Jiang, H. / An, Z. / Wang, J. / Yilma, T.D. / Shi, Y. / Liu, W.J. / Liang, M. / Qin, C. / Gao, G.F. / Yan, J.
History
DepositionSep 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NSmGnGc
B: Heavy chain of Fab R12
C: Light chain of Fab R12
D: NSmGnGc
E: Heavy chain of Fab R12
F: Light chain of Fab R12


Theoretical massNumber of molelcules
Total (without water)165,6106
Polymers165,6106
Non-polymers00
Water3,999222
1
A: NSmGnGc
B: Heavy chain of Fab R12
C: Light chain of Fab R12


Theoretical massNumber of molelcules
Total (without water)82,8053
Polymers82,8053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: NSmGnGc
E: Heavy chain of Fab R12
F: Light chain of Fab R12


Theoretical massNumber of molelcules
Total (without water)82,8053
Polymers82,8053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.756, 108.070, 107.418
Angle α, β, γ (deg.)90.00, 90.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NSmGnGc / glycoprotein N / Gn


Mass: 34940.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rift valley fever virus
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: H9BSP3, UniProt: P03518*PLUS
#2: Antibody Heavy chain of Fab R12


Mass: 24334.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals)
#3: Antibody Light chain of Fab R12


Mass: 23530.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mammalia (mammals)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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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: 3.48 Å3/Da / Density % sol: 64.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M TRIS, PH8, 1.2M Na/K tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 61396 / % possible obs: 99.8 % / Redundancy: 4.7 % / Net I/σ(I): 11.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.5 % / Num. unique obs: 6102 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.7→48.271 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.15
RfactorNum. reflection% reflection
Rfree0.258 2811 4.95 %
Rwork0.225 --
obs0.2267 56742 91.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11306 0 0 222 11528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311606
X-RAY DIFFRACTIONf_angle_d0.62615772
X-RAY DIFFRACTIONf_dihedral_angle_d20.3054294
X-RAY DIFFRACTIONf_chiral_restr0.0431732
X-RAY DIFFRACTIONf_plane_restr0.0052020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6953-2.74180.3139540.31341134X-RAY DIFFRACTION39
2.7418-2.79160.3448750.3041457X-RAY DIFFRACTION50
2.7916-2.84530.32541030.30661965X-RAY DIFFRACTION68
2.8453-2.90340.34591410.30412560X-RAY DIFFRACTION87
2.9034-2.96650.371270.29272840X-RAY DIFFRACTION96
2.9665-3.03550.30431880.28062830X-RAY DIFFRACTION99
3.0355-3.11140.33711200.27122940X-RAY DIFFRACTION100
3.1114-3.19550.35841150.26022959X-RAY DIFFRACTION100
3.1955-3.28950.2691840.26272912X-RAY DIFFRACTION100
3.2895-3.39570.27721920.24982875X-RAY DIFFRACTION100
3.3957-3.5170.31461580.23252901X-RAY DIFFRACTION100
3.517-3.65780.2461370.23022951X-RAY DIFFRACTION100
3.6578-3.82420.25291130.21982985X-RAY DIFFRACTION100
3.8242-4.02570.24991440.21672939X-RAY DIFFRACTION100
4.0257-4.27780.2361860.19722901X-RAY DIFFRACTION100
4.2778-4.60790.21731470.17792919X-RAY DIFFRACTION100
4.6079-5.07110.20891270.17622989X-RAY DIFFRACTION100
5.0711-5.80390.21191530.19732951X-RAY DIFFRACTION100
5.8039-7.30820.27441890.21982922X-RAY DIFFRACTION100
7.3082-48.27920.19531580.21063001X-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)
10.5029-0.2484-0.49450.44360.33440.69020.08180.002-0.1035-0.0813-0.0790.0167-0.00840.0539-0.00070.16320.0175-0.02080.2116-0.06970.196820.3144-10.137725.0148
20.6670.07560.35440.15310.34040.78070.03160.0059-0.02060.03290.0177-0.06870.05770.0318-00.2294-0.03110.00250.13850.00650.174633.36535.508872.6478
30.653-0.09760.58980.0152-0.11621.0965-0.09010.08790.02420.00270.01110.00810.00230.110700.20950.0035-0.01350.176-0.01890.176447.14658.687462.8657
40.8573-0.18140.25990.4088-0.3790.5470.03960.08050.212-0.0512-0.0718-0.0276-0.09970.1088-0.01380.155-0.01950.0210.18760.07570.206728.402444.6259-16.6608
50.8377-0.2961-0.48840.21490.11370.63210.0102-0.2427-0.11230.07290.0571-0.1158-0.01070.25950.10960.3068-0.036-0.04830.26410.02750.21415.223632.118732.5089
60.6131-0.0207-0.53320.0056-0.03260.8073-0.01990.02290.0232-0.03430.0272-0.0285-0.0021-0.081-00.18920.00230.01670.12860.00870.16921.455628.422522.753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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