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- PDB-6iw5: Crystal structure of YFV-China sE in prefusion state -

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Basic information

Entry
Database: PDB / ID: 6iw5
TitleCrystal structure of YFV-China sE in prefusion state
ComponentsEnvelope proteinViral envelope
KeywordsVIRAL PROTEIN / Yellow fever virus / Neutralizing monoclonal antibody / Envelope protein / Flavivirus
Function / homology
Function and homology information


host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 ...Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesYellow fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLu, X.S. / Xiao, H.X. / Li, S.H. / Pang, X.F.
CitationJournal: Cell Rep / Year: 2019
Title: Double Lock of a Human Neutralizing and Protective Monoclonal Antibody Targeting the Yellow Fever Virus Envelope.
Authors: Lu, X. / Xiao, H. / Li, S. / Pang, X. / Song, J. / Liu, S. / Cheng, H. / Li, Y. / Wang, X. / Huang, C. / Guo, T. / Ter Meulen, J. / Daffis, S. / Yan, J. / Dai, L. / Rao, Z. / Klenk, H.D. / ...Authors: Lu, X. / Xiao, H. / Li, S. / Pang, X. / Song, J. / Liu, S. / Cheng, H. / Li, Y. / Wang, X. / Huang, C. / Guo, T. / Ter Meulen, J. / Daffis, S. / Yan, J. / Dai, L. / Rao, Z. / Klenk, H.D. / Qi, J. / Shi, Y. / Gao, G.F.
History
DepositionDec 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope protein
B: Envelope protein
C: Envelope protein
D: Envelope protein


Theoretical massNumber of molelcules
Total (without water)171,1054
Polymers171,1054
Non-polymers00
Water2,756153
1
A: Envelope protein

B: Envelope protein


Theoretical massNumber of molelcules
Total (without water)85,5532
Polymers85,5532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y+1/2,-z+21
Buried area2220 Å2
ΔGint-14 kcal/mol
Surface area36370 Å2
MethodPISA
2
C: Envelope protein

D: Envelope protein


Theoretical massNumber of molelcules
Total (without water)85,5532
Polymers85,5532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y+1/2,-z+21
Buried area2110 Å2
ΔGint-15 kcal/mol
Surface area36990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.785, 121.362, 101.581
Angle α, β, γ (deg.)90.00, 93.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Envelope protein / Viral envelope


Mass: 42776.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yellow fever virus / Gene: E / Production host: Escherichia coli (E. coli) / References: UniProt: Q89292
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 55335 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Redundancy: 6.7 % / Net I/σ(I): 13.8
Reflection shellResolution: 2.5→50 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.5→46.78 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.75
RfactorNum. reflection% reflection
Rfree0.2916 2202 5.03 %
Rwork0.2365 --
obs0.2393 43780 78.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11980 0 0 153 12133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612244
X-RAY DIFFRACTIONf_angle_d1.31316580
X-RAY DIFFRACTIONf_dihedral_angle_d14.7374404
X-RAY DIFFRACTIONf_chiral_restr0.0541880
X-RAY DIFFRACTIONf_plane_restr0.0052140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4919-2.54610.4076530.3381801X-RAY DIFFRACTION25
2.5461-2.60530.4295670.31281226X-RAY DIFFRACTION37
2.6053-2.67050.3625820.32541634X-RAY DIFFRACTION50
2.6705-2.74270.3596900.32531905X-RAY DIFFRACTION58
2.7427-2.82340.3644990.31642171X-RAY DIFFRACTION65
2.8234-2.91450.35131370.30152300X-RAY DIFFRACTION71
2.9145-3.01860.39881510.29952537X-RAY DIFFRACTION77
3.0186-3.13950.33021710.29462773X-RAY DIFFRACTION85
3.1395-3.28230.34641500.28123109X-RAY DIFFRACTION93
3.2823-3.45530.28861870.2633239X-RAY DIFFRACTION99
3.4553-3.67170.34291660.24413293X-RAY DIFFRACTION100
3.6717-3.95510.30431500.23013304X-RAY DIFFRACTION100
3.9551-4.35280.26121970.20243280X-RAY DIFFRACTION100
4.3528-4.98210.19431570.18513313X-RAY DIFFRACTION100
4.9821-6.27450.28771530.20473356X-RAY DIFFRACTION100
6.2745-46.78860.23021920.19043337X-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)
10.08460.07160.03710.19560.05320.06050.02890.0044-0.02350.11560.0177-0.06230.07070.04630.03280.0580.0081-0.03470.1014-0.03420.12837.401924.2163104.6713
2-0.0026-0.0399-0.00920.1198-0.02170.02220.02340.0453-0.0133-0.1648-0.02280.03960.00160.0054-0.01150.08540.0562-0.06560.08950.0346-0.0206-2.55911.581764.566
30.01780.089-0.09160.1302-0.00030.1908-0.10180.1998-0.1873-0.2967-0.057-0.3750.16510.0381-0.31520.0362-0.03990.2171-0.0216-0.08090.064319.87653.024660.5503
40.02740.0065-0.03870.07520.03410.045-0.0634-0.0048-0.08590.0957-0.0189-0.0436-0.1238-0.027-0.09090.16110.0441-0.06740.14670.04780.116-24.817429.5247104.1105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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