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- PDB-6iec: Structure of RVFV Gn and human monoclonal antibody R17 -

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Basic information

Entry
Database: PDB / ID: 6iec
TitleStructure of RVFV Gn and human monoclonal antibody R17
Components
  • NSmGnGc
  • R17 H chain
  • R17 L chain
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
Similarity search - Domain/homology
Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesRift valley fever virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 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 13, 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
H: R17 H chain
L: R17 L chain
B: NSmGnGc
C: R17 H chain
D: R17 L chain
E: NSmGnGc
F: R17 H chain
G: R17 L chain
I: NSmGnGc
J: R17 H chain
K: R17 L chain


Theoretical massNumber of molelcules
Total (without water)237,67912
Polymers237,67912
Non-polymers00
Water0
1
A: NSmGnGc
H: R17 H chain
L: R17 L chain


Theoretical massNumber of molelcules
Total (without water)59,4203
Polymers59,4203
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NSmGnGc
C: R17 H chain
D: R17 L chain


Theoretical massNumber of molelcules
Total (without water)59,4203
Polymers59,4203
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: NSmGnGc
F: R17 H chain
G: R17 L chain


Theoretical massNumber of molelcules
Total (without water)59,4203
Polymers59,4203
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: NSmGnGc
J: R17 H chain
K: R17 L chain


Theoretical massNumber of molelcules
Total (without water)59,4203
Polymers59,4203
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)198.009, 198.009, 164.467
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein
NSmGnGc / glycoprotein N / Gn


Mass: 34940.828 Da / Num. of mol.: 4
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
R17 H chain


Mass: 12611.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
R17 L chain


Mass: 11867.927 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium sulfate, 0.1M Tris 7.5, 20% w/v PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 58821 / % possible obs: 97.2 % / Redundancy: 6.5 % / CC1/2: 0.986 / Rpim(I) all: 0.09 / Net I/σ(I): 7.3
Reflection shellResolution: 3.2→3.31 Å / Mean I/σ(I) obs: 2 / CC1/2: 0.81 / Rpim(I) all: 0.0302

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.2→47.56 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.1
RfactorNum. reflection% reflection
Rfree0.2808 2634 5.04 %
Rwork0.2408 --
obs0.2428 52279 86.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16184 0 0 0 16184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316604
X-RAY DIFFRACTIONf_angle_d0.70722496
X-RAY DIFFRACTIONf_dihedral_angle_d12.9546160
X-RAY DIFFRACTIONf_chiral_restr0.0452396
X-RAY DIFFRACTIONf_plane_restr0.0062912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1977-3.25590.37721130.36051901X-RAY DIFFRACTION64
3.2559-3.31850.40041030.33991992X-RAY DIFFRACTION67
3.3185-3.38620.3545920.3232152X-RAY DIFFRACTION71
3.3862-3.45980.35151070.312211X-RAY DIFFRACTION73
3.4598-3.54030.30251120.29752307X-RAY DIFFRACTION76
3.5403-3.62880.38141200.30252466X-RAY DIFFRACTION82
3.6288-3.72680.37061270.28852565X-RAY DIFFRACTION84
3.7268-3.83650.37171350.29952659X-RAY DIFFRACTION88
3.8365-3.96020.32671550.27462724X-RAY DIFFRACTION90
3.9602-4.10170.29991500.26242719X-RAY DIFFRACTION92
4.1017-4.26580.29591830.2222799X-RAY DIFFRACTION93
4.2658-4.45980.23541680.21682811X-RAY DIFFRACTION94
4.4598-4.69480.2061780.19642888X-RAY DIFFRACTION96
4.6948-4.98860.2381290.20762928X-RAY DIFFRACTION96
4.9886-5.37330.26171660.21312901X-RAY DIFFRACTION96
5.3733-5.91320.29461570.23072905X-RAY DIFFRACTION96
5.9132-6.76670.26661450.23672905X-RAY DIFFRACTION95
6.7667-8.51730.26761360.21912929X-RAY DIFFRACTION96
8.5173-47.56550.22591580.19122883X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -136.1501 Å / Origin y: 358.7399 Å / Origin z: -50.157 Å
111213212223313233
T0.3942 Å2-0.0053 Å20.0202 Å2-0.3603 Å2-0.0056 Å2--0.395 Å2
L0.0547 °2-0.042 °2-0.0166 °2--0.0722 °20.0197 °2--0.0202 °2
S-0.01 Å °0.0113 Å °-0.0461 Å °-0.0036 Å °0.0181 Å °0.0214 Å °0.0113 Å °-0.0184 Å °-0 Å °
Refinement TLS groupSelection details: all

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