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- PDB-8gpt: YFV_E_YD6scFv_postfusion -

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Basic information

Entry
Database: PDB / ID: 8gpt
TitleYFV_E_YD6scFv_postfusion
Components
  • Envelope protein
  • YD6_VH
  • YD6_VL
KeywordsANTIVIRAL PROTEIN / Yellow fever virus / neutralizing antibody / human antibody
Function / homology
Function and homology information


helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / virion membrane / membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 ...Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesYellow fever virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsLi, Y. / Wu, L. / Qi, J. / Yan, J. / Gao, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Innovation (N Y) / Year: 2022
Title: A neutralizing-protective supersite of human monoclonal antibodies for yellow fever virus.
Authors: Li, Y. / Chen, Z. / Wu, L. / Dai, L. / Qi, J. / Chai, Y. / Li, S. / Wang, Q. / Tong, Z. / Ma, S. / Duan, X. / Ren, S. / Song, R. / Liang, M. / Liu, W. / Yan, J. / Gao, G.F.
History
DepositionAug 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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: Envelope protein
D: YD6_VH
E: YD6_VL
B: Envelope protein
F: YD6_VH
G: YD6_VL
C: Envelope protein
H: YD6_VH
I: YD6_VL


Theoretical massNumber of molelcules
Total (without water)204,1159
Polymers204,1159
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23280 Å2
ΔGint-82 kcal/mol
Surface area74460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.536, 150.866, 126.418
Angle α, β, γ (deg.)90.000, 111.999, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Envelope protein


Mass: 43249.832 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yellow fever virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q89292
#2: Antibody YD6_VH


Mass: 12939.524 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Antibody YD6_VL


Mass: 11849.030 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
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

CrystalDensity Matthews: 4.92 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: in 0.1M ammonium sulfate, 0.3M sodium formate, 0.1M sodium acetate, 3% (w/v) PGA-LM, 5% (w/v) PEG 8,000, pH5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.07→50 Å / Num. obs: 70474 / % possible obs: 98.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 67.14 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.3
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 6984 / CC1/2: 0.642

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JHL

5jhl


Resolution: 3.07→49.62 Å / SU ML: 0.2486 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.2262
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2468 3176 4.88 %
Rwork0.2112 61887 -
obs0.2129 65063 87.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.64 Å2
Refinement stepCycle: LAST / Resolution: 3.07→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14130 0 0 0 14130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004114418
X-RAY DIFFRACTIONf_angle_d0.671819548
X-RAY DIFFRACTIONf_chiral_restr0.04972193
X-RAY DIFFRACTIONf_plane_restr0.00432505
X-RAY DIFFRACTIONf_dihedral_angle_d15.23425145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.07-3.110.3773260.3306463X-RAY DIFFRACTION15.24
3.11-3.160.3702800.32361161X-RAY DIFFRACTION38.64
3.16-3.210.3487930.31411780X-RAY DIFFRACTION58.26
3.21-3.270.37851100.30921930X-RAY DIFFRACTION63.12
3.27-3.330.39411030.30192370X-RAY DIFFRACTION76.59
3.33-3.390.31471400.28532671X-RAY DIFFRACTION88.04
3.39-3.460.30561490.26772871X-RAY DIFFRACTION93.93
3.46-3.540.30011710.24612940X-RAY DIFFRACTION97.28
3.54-3.620.24151710.24663033X-RAY DIFFRACTION98.37
3.62-3.710.2751460.24783057X-RAY DIFFRACTION98.83
3.71-3.810.24931520.2393022X-RAY DIFFRACTION98.76
3.81-3.920.26011390.2353053X-RAY DIFFRACTION99.01
3.92-4.050.26471490.20843032X-RAY DIFFRACTION99.19
4.05-4.190.24221540.20783068X-RAY DIFFRACTION99.32
4.19-4.360.20661530.18423039X-RAY DIFFRACTION99.16
4.36-4.560.19361470.16623047X-RAY DIFFRACTION98.4
4.56-4.80.2031390.16762948X-RAY DIFFRACTION95.96
4.8-5.10.211650.1763033X-RAY DIFFRACTION98.98
5.1-5.50.23021650.18073098X-RAY DIFFRACTION99.79
5.5-6.050.24391650.19453042X-RAY DIFFRACTION99.75
6.05-6.920.24561500.20923089X-RAY DIFFRACTION99.42
6.92-8.710.20461710.19113045X-RAY DIFFRACTION98.83
8.71-49.620.24251380.19563095X-RAY DIFFRACTION96.94
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)
11.9657422504-0.177847864275-1.106046240390.3490975004770.2042555457251.42476960289-0.128317447248-0.287934666774-0.1741475376610.1314941523460.06223808344210.144892937010.224934676038-0.06997673309440.1175437388540.386197134938-0.02108721617740.01915845590550.2592737619010.06289921355150.375592485814-55.03369111637.836391765234.0710872568
22.0571493267-0.0487306876643-0.6674662568330.302456688774-0.08867116329260.6787247997330.0731353257395-0.1650472142320.3667921357880.1312809605490.05421829642520.139745408876-0.179215954441-0.15411921307-0.1505269013550.4014310343130.03428530951360.03558985567950.312925842507-0.05255836796610.422384907063-55.010999926363.504155658833.6819299335
32.189415629490.343243713744-0.9774615399940.598457186862-0.2561327309241.09506685577-0.09252664148220.19762552993-0.0820404666919-0.07426171447670.0516748437240.2170523470990.0811505102587-0.3848455278360.03499290494870.273128212211-0.0149700558058-0.08267563749730.3487299746570.01720257477070.318496418375-66.227724333350.435672124714.4588288923
42.460129697780.7640357729740.465486732983.297766653561.133127673783.59284911977-0.2492882583320.57631864965-0.416740790491-0.286330784560.115231732138-0.153334222750.2979798340460.2430910090950.1448600322770.477218076586-0.1026814774740.08400448020010.432193948019-0.1434698995180.464953424757-23.725637001619.2747651586-11.5414253806
52.643812799381.36350674474-0.1340328856023.613236710791.171769352152.20933474471-0.1474645351610.25301998861-0.3938957332450.0172987161259-0.02717533564080.5466341766910.373421237222-0.6029065182680.1081915768840.476329296455-0.1132503065680.02946983208050.353179537546-0.1189785654590.638969387562-44.378383774917.2908826524-5.34623546018
64.19835460661-0.5951368157971.452687844662.0106343974-0.5561180752754.11964888941-0.0788849604047-0.5558387861860.3733628685510.0427989200495-0.0343069097238-0.2283762041580.11007360150.5988213800780.05626571662660.2825434604730.01157538347180.02379796414010.473632097936-0.06846572885420.2755963693342.2221462148352.068683121633.8001516772
73.13543429604-0.1085048909450.09238244152031.38370942933-0.2968648292564.24992772571-0.0736089972918-0.9239830618570.04310871994720.4538281250130.07265693108730.1030586249390.091290305475-0.3926991917350.007861119835770.347751210021-0.0195533467974-0.009934308106620.671949970964-0.09589963925410.310585142012-13.952841054450.199713121447.9857154339
82.10193998914-0.0473298704716-0.1881439542743.21305263342-1.617646208621.467570210640.05600819338040.6307454786170.67585918366-0.270790961246-0.0528223547222-0.374911954128-0.164130492054-0.01571515068910.02442843990280.4212144844650.06092977648430.03186773707530.451280189070.1740122067180.536790268564-25.087894158679.4642317267-14.6652655102
92.27116904575-0.2661835238470.1916325564122.54077863058-0.8433364201812.184124595110.0137872525085-0.1533629371380.5704536089140.2085179422490.03905189583740.588378584531-0.367604704293-0.465260936173-0.06023486583250.510955215280.1378123998970.04000437718650.517916867460.1619968072860.617772755943-43.653406056684.4989948473-4.6726757715
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA2 - 3981 - 391
22chain BBD2 - 3981 - 391
33chain CCG2 - 3981 - 391
44chain DDB1 - 1171 - 117
55chain EEC1 - 1121 - 112
66chain FFE1 - 1171 - 117
77chain GGF1 - 1121 - 112
88chain HHH1 - 1171 - 117
99chain III1 - 1121 - 112

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