[English] 日本語
Yorodumi
- PDB-8gpx: YFV_E_YD73Fab_postfusion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gpx
TitleYFV_E_YD73Fab_postfusion
Components
  • Envelope proteinViral envelope
  • YD73Fab_H
  • YD73Fab_K
KeywordsANTIVIRAL PROTEIN / Yellow fever virus / neutralizing antibody / human antibody
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
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 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
Components

#1: Protein Envelope protein / Viral envelope


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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more