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- PDB-6iea: Structure of RVFV Gn and human monoclonal antibody R13 -

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Basic information

Entry
Database: PDB / ID: 6iea
TitleStructure of RVFV Gn and human monoclonal antibody R13
Components
  • NSmGnGc
  • R13 H chain
  • R13 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 / 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
DI(HYDROXYETHYL)ETHER / Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesRift valley fever virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 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
L: R13 L chain
H: R13 H chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4205
Polymers82,2223
Non-polymers1982
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-26 kcal/mol
Surface area32380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.210, 97.107, 112.504
Angle α, β, γ (deg.)90.00, 96.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NSmGnGc / glycoprotein N / Gn


Mass: 34940.828 Da / Num. of mol.: 1
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

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Antibody , 2 types, 2 molecules LH

#2: Antibody R13 L chain


Mass: 23369.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody R13 H chain


Mass: 23910.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 378 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M magnesium formate, 20% w/v PEG 3350

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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: Apr 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 61226 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.992 / Rpim(I) all: 0.041 / Net I/σ(I): 16.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2 / CC1/2: 0.886 / Rpim(I) all: 0.365 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2→48.454 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.04
RfactorNum. reflection% reflection
Rfree0.2254 2431 4.71 %
Rwork0.1808 --
obs0.1829 51622 84.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→48.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5548 0 13 376 5937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085722
X-RAY DIFFRACTIONf_angle_d1.0057785
X-RAY DIFFRACTIONf_dihedral_angle_d4.0713988
X-RAY DIFFRACTIONf_chiral_restr0.056856
X-RAY DIFFRACTIONf_plane_restr0.006993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04090.2931550.22441506X-RAY DIFFRACTION44
2.0409-2.08530.3243890.21641743X-RAY DIFFRACTION52
2.0853-2.13380.24811010.20952004X-RAY DIFFRACTION59
2.1338-2.18710.26391010.20822221X-RAY DIFFRACTION65
2.1871-2.24630.27881360.21152407X-RAY DIFFRACTION71
2.2463-2.31240.2341210.20252698X-RAY DIFFRACTION79
2.3124-2.3870.25711300.20782882X-RAY DIFFRACTION85
2.387-2.47230.29211470.21093103X-RAY DIFFRACTION91
2.4723-2.57130.22961730.20243297X-RAY DIFFRACTION98
2.5713-2.68830.26261960.20673337X-RAY DIFFRACTION99
2.6883-2.830.24021740.2043426X-RAY DIFFRACTION100
2.83-3.00730.26211820.2053402X-RAY DIFFRACTION100
3.0073-3.23950.23551510.19553422X-RAY DIFFRACTION100
3.2395-3.56540.25341590.18613416X-RAY DIFFRACTION100
3.5654-4.08110.20361540.15873424X-RAY DIFFRACTION100
4.0811-5.14080.16731820.13143439X-RAY DIFFRACTION100
5.1408-48.46830.18081800.15933464X-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)
10.4835-0.12330.15282.465-0.70882.1874-0.0191-0.0766-0.01590.3849-0.0566-0.1242-0.26530.06550.05280.1774-0.01810.01620.106-0.01190.168225.41230.2699164.188
20.2176-0.0443-0.76970.79590.03662.70450.01630.3049-0.0715-0.2436-0.02650.08290.2955-0.47360.00210.19820.0263-0.05040.3792-0.06930.239620.5395-17.8633114.6149
30.0604-0.10650.21341.04230.61691.59630.10860.337-0.0451-0.2927-0.0453-0.0069-0.34580.1575-0.03290.19730.06820.03170.4587-0.02280.232729.9043-2.1888116.9501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:315 )A1 - 315
2X-RAY DIFFRACTION2( CHAIN L AND RESID 2:209 )L2 - 209
3X-RAY DIFFRACTION3( CHAIN H AND RESID 1:225 )H1 - 225

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