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- PDB-8gpx: YFV_E_YD73Fab_postfusion -

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Basic information

Entry
Database: PDB / ID: 8gpx
TitleYFV_E_YD73Fab_postfusion
Components
  • Envelope protein
  • YD73Fab_H
  • YD73Fab_K
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: 3.8 Å
AuthorsLi, Y. / Wu, L. / Chai, Y. / 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 30, 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
E: Envelope protein
H: YD73Fab_H
L: YD73Fab_K


Theoretical massNumber of molelcules
Total (without water)91,4103
Polymers91,4103
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.874, 102.874, 178.663
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z

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Components

#1: Protein Envelope protein


Mass: 43249.832 Da / Num. of mol.: 1
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 YD73Fab_H


Mass: 24333.131 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 YD73Fab_K


Mass: 23827.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M imidazole malate, pH 5.5, and 33% (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 11224 / % possible obs: 99.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 58.55 Å2 / Rmerge(I) obs: 0.188 / Net I/σ(I): 8.082
Reflection shellResolution: 3.8→3.94 Å / Rmerge(I) obs: 0.866 / Num. unique obs: 1088 / CC1/2: 0.627

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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: 3.8→39.93 Å / SU ML: 0.2717 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.3702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3059 560 5.1 %
Rwork0.2612 10428 -
obs0.2635 10988 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.17 Å2
Refinement stepCycle: LAST / Resolution: 3.8→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6180 0 0 0 6180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216318
X-RAY DIFFRACTIONf_angle_d0.54038589
X-RAY DIFFRACTIONf_chiral_restr0.0437968
X-RAY DIFFRACTIONf_plane_restr0.0041101
X-RAY DIFFRACTIONf_dihedral_angle_d13.43252263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.180.34571470.28592358X-RAY DIFFRACTION91.22
4.18-4.790.28851230.24932646X-RAY DIFFRACTION99.5
4.79-6.020.3291380.25952654X-RAY DIFFRACTION99.32
6.03-39.930.27211520.25722770X-RAY DIFFRACTION99.29
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)
10.5861389640270.1286933778570.3571518462660.6320608842230.04666158020760.448141712932-0.0207571231829-0.177180841766-0.06286080332270.202188571532-0.1172429547390.0722057983994-0.138521476998-0.1975001005270.1491632698220.43058346401-0.0002021835641570.10010692270.494150481272-0.02096500031330.42500003754938.9694985045-34.056521640772.631685662
20.201372116554-0.106663217066-0.02546707887890.169699784163-0.06811584278960.7183062135240.158526688716-0.204851795752-0.2966573651850.33613248818-0.03413830510460.3319057255630.151240908053-0.296030209677-0.08513412391790.935405826768-0.1597924478260.1996199951120.8019831615620.1785578009070.61213958182241.9784858518-50.567195593892.1576415234
30.898978390493-0.0607895748374-0.06399855145461.21763477955-0.4017936556711.858348958270.08522084220360.0005948731244510.0929682596423-0.38686394813-0.6421808588540.210147316188-0.0243578833233-0.03863377573210.4310853354520.4459200518490.177353606504-0.1007375810470.38333034767-0.2011166639660.44239317706917.7025628186-37.439013688723.9743843019
42.380061621961.04128111885-0.04233712892570.8548664180490.04104618063863.082487877431.180455935750.4129779837610.3010363825750.0739248257610.64905570163-0.2322562912110.1630205625320.725120576933-0.5644368887590.1924731761280.09684268046160.2488330600350.5544137080330.03808524091720.17485213196-9.32165791487-15.467793751210.8948242194
50.207977651959-0.142018313908-0.09849842619880.07690658977930.06614568260590.0388529404412-0.0368807913017-0.0393716270606-0.2308424000740.198872576052-0.02518020146740.01092640789380.00539755038899-0.1264863460970.02897935230760.537876855530.113719277490.2551874516220.132106803588-0.2786052546540.1823398240341.76427849591-23.61876162243.0914296515
61.44801359313-0.648725439980.2899788184571.009050801060.4253015284720.45296200876-0.170895792817-0.1553227626-0.109968699406-0.0561594740744-0.1098503431710.29765150007-0.0833890900826-0.2424553447860.1091872275050.15434668545-0.00626204018232-0.09626915496830.259403685755-0.1256773341630.52248563312111.4977239944-27.989507136238.962708501
71.05269189824-0.8693650862930.2834191087260.8663015453640.221508894251.16606594671-0.119017571569-0.112766418054-0.01284874823360.267489634952-0.1342713346060.09635247105860.08151767796410.09086462158060.04179141416330.450521835473-0.05661321607070.04655172597270.0745713804971-0.08808142457850.20342226479115.2270730384-23.093640108244.0858576404
80.710759976499-0.786808160968-0.1031010666321.918165507090.2944330758110.3516385335120.002836308639530.0680108703550.1073895963840.133337708891-0.04799437613070.1305281570650.0513429732779-0.2404764071750.008609598506650.29476089002-0.038424100285-0.04378227997310.265019595656-0.119570357340.5044185763919.50985084126-27.080859639737.4022943442
90.0644144284638-0.0889802014475-0.02422296716720.1768482898750.0243079139335-0.000357457943607-0.08689261878790.1329738537760.06326931884830.008127460806240.26433904704-0.270276737983-0.0632892451172-0.134859546737-0.00931248716450.307884988476-0.1269233999860.2142814799480.3651144489480.213585500460.375261471548-10.5756560635-13.6704024535.881676062
101.04460458552-0.1962291323940.332535911450.8103952463370.01341134890062.263930912030.2666159323310.3170770320760.224236611281-0.3581474637010.2148738646220.175084950167-0.0496339018058-0.13320872724-0.09350871942530.335229208513-0.0132918883415-0.1317002882730.4840750568640.1475138900180.535740018633-20.4925744519-19.030498278914.0691131499
110.0131121748051-0.0896514179769-0.07225713876710.4404265247350.2980891521920.1936029211320.18908149043-0.0599409262459-0.313497824851-0.103181095601-0.1562552866780.2361655088440.30902840708-0.0415399536745-0.03510451682740.2887877819590.0807365591268-0.6676194847330.3188820648790.2613737475180.676708395237-20.8966863876-26.67205232225.8770670515
121.340306119260.09424677967310.2805776612470.5715234003440.3380528567311.13779877766-0.04767010346080.1368144299990.309659000195-0.3112101329550.05939726251720.1924180122560.174315502214-0.242921331305-0.05208913362020.455888874196-0.052454350993-0.05065250577370.3777270486680.1697006574560.396166601322-18.7095845418-21.726267419220.8221662752
130.453709036522-0.0664112547303-0.2524801316930.584368243573-0.04537645764840.1442235492490.0909535272489-0.0469979231317-0.106585885844-0.125609375530.07936935243340.2879391292280.1462428934310.0132909790193-0.0576813688510.333009169543-0.0557494316189-0.06034681304680.9309795813790.2037638914130.465000132209-27.9050370125-18.430277155825.8039889668
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 3 through 243 )EA3 - 2431 - 227
22chain 'E' and (resid 244 through 394 )EA244 - 394228 - 376
33chain 'H' and (resid 1 through 118 )HB1 - 1181 - 118
44chain 'H' and (resid 119 through 226 )HB119 - 226119 - 220
55chain 'L' and (resid 2 through 18 )LC2 - 181 - 17
66chain 'L' and (resid 19 through 49 )LC19 - 4918 - 48
77chain 'L' and (resid 50 through 76 )LC50 - 7649 - 75
88chain 'L' and (resid 77 through 104 )LC77 - 10476 - 103
99chain 'L' and (resid 105 through 117 )LC105 - 117104 - 116
1010chain 'L' and (resid 118 through 141 )LC118 - 141117 - 140
1111chain 'L' and (resid 142 through 162 )LC142 - 162141 - 161
1212chain 'L' and (resid 163 through 199 )LC163 - 199162 - 198
1313chain 'L' and (resid 200 through 215 )LC200 - 215199 - 214

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