[English] 日本語
Yorodumi
- PDB-5vig: Crystal structure of anti-Zika antibody Z006 bound to Zika virus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vig
TitleCrystal structure of anti-Zika antibody Z006 bound to Zika virus envelope protein DIII
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • Zika virus envelope protein DIII
KeywordsIMMUNE SYSTEM / antibody / Fab / Zika / Dengue / recurrent / neutralizing
Function / homology
Function and homology information


immunoglobulin complex / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / adaptive immune response / membrane => GO:0016020 ...immunoglobulin complex / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / adaptive immune response / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / extracellular region / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C ...Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / 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 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Helicase superfamily 1/2, ATP-binding domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / Core protein / Core protein / Immunoglobulin kappa light chain / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Zika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsKeeffe, J.R. / West Jr., A.P. / Gristick, H.B. / Bjorkman, P.J.
CitationJournal: Cell / Year: 2017
Title: Recurrent Potent Human Neutralizing Antibodies to Zika Virus in Brazil and Mexico.
Authors: Robbiani, D.F. / Bozzacco, L. / Keeffe, J.R. / Khouri, R. / Olsen, P.C. / Gazumyan, A. / Schaefer-Babajew, D. / Avila-Rios, S. / Nogueira, L. / Patel, R. / Azzopardi, S.A. / Uhl, L.F.K. / ...Authors: Robbiani, D.F. / Bozzacco, L. / Keeffe, J.R. / Khouri, R. / Olsen, P.C. / Gazumyan, A. / Schaefer-Babajew, D. / Avila-Rios, S. / Nogueira, L. / Patel, R. / Azzopardi, S.A. / Uhl, L.F.K. / Saeed, M. / Sevilla-Reyes, E.E. / Agudelo, M. / Yao, K.H. / Golijanin, J. / Gristick, H.B. / Lee, Y.E. / Hurley, A. / Caskey, M. / Pai, J. / Oliveira, T. / Wunder, E.A. / Sacramento, G. / Nery, N. / Orge, C. / Costa, F. / Reis, M.G. / Thomas, N.M. / Eisenreich, T. / Weinberger, D.M. / de Almeida, A.R.P. / West, A.P. / Rice, C.M. / Bjorkman, P.J. / Reyes-Teran, G. / Ko, A.I. / MacDonald, M.R. / Nussenzweig, M.C.
History
DepositionApr 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
Z: Zika virus envelope protein DIII
A: Fab heavy chain
B: Fab light chain
G: Zika virus envelope protein DIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,1037
Polymers120,9146
Non-polymers1891
Water0
1
H: Fab heavy chain
L: Fab light chain
Z: Zika virus envelope protein DIII


Theoretical massNumber of molelcules
Total (without water)60,4573
Polymers60,4573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-27 kcal/mol
Surface area22640 Å2
MethodPISA
2
A: Fab heavy chain
B: Fab light chain
G: Zika virus envelope protein DIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6464
Polymers60,4573
Non-polymers1891
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-26 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)385.082, 385.082, 56.640
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

-
Components

#1: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 25110.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) / References: UniProt: S6B291
#2: Antibody Fab light chain / Fragment antigen-binding / Immunoglobulin kappa light chain EU


Mass: 23411.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) / References: UniProt: P0DOX7
#3: Protein Zika virus envelope protein DIII


Mass: 11935.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Strain: Mr 766 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1I9ZK43, UniProt: A0A192GPS0*PLUS
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.2 % / Mosaicity: 0.29 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10% isopropanol, 0.1M sodium citrate tribasic dihydrate pH 5.0, 26% PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2016
RadiationMonochromator: double crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→96.27 Å / Num. obs: 34940 / % possible obs: 99 % / Redundancy: 5.4 % / Biso Wilson estimate: 77.58 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.062 / Rrim(I) all: 0.149 / Net I/σ(I): 7.5 / Num. measured all: 189075 / Scaling rejects: 116
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.9-3.040.9542528746600.5920.4411.0541.799.6
9.62-96.270.07353179790.9840.0340.08116.797.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.29data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.749 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 1566 4.97 %
Rwork0.2119 29949 -
obs0.2142 31515 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 234.79 Å2 / Biso mean: 103.7802 Å2 / Biso min: 63.85 Å2
Refinement stepCycle: final / Resolution: 3→29.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7892 0 13 0 7905
Biso mean--138.38 --
Num. residues----1050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078094
X-RAY DIFFRACTIONf_angle_d0.84411049
X-RAY DIFFRACTIONf_chiral_restr0.051274
X-RAY DIFFRACTIONf_plane_restr0.0071409
X-RAY DIFFRACTIONf_dihedral_angle_d13.3444791
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.09680.38361540.330227132867100
3.0968-3.20730.36091290.314627442873100
3.2073-3.33560.36551390.30682742288199
3.3356-3.48720.32981330.28262713284699
3.4872-3.67070.32761600.264726912851100
3.6707-3.90020.32071530.24192690284398
3.9002-4.20060.26341370.210527472884100
4.2006-4.62190.1921470.160927502897100
4.6219-5.28740.19611430.15282699284298
5.2874-6.64930.23261240.19052725284998
6.6493-29.75050.22111470.18622735288297
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)
11.1244-0.7675-0.8221.83980.60930.78640.2820.3284-0.60750.3321-0.1742-0.0444-0.3069-0.5453-0.00840.93760.2808-0.46570.3762-0.3341.269823.688-87.2304-21.1711
22.6820.0699-0.014.0243-2.70423.75290.15890.6404-0.2486-0.4684-0.24881.26280.4272-0.90370.09070.95540.2925-0.33921.1366-0.60331.5916-7.0454-94.3805-33.8707
30.8522-0.5633-0.31511.09310.16580.12430.1410.306-0.3076-0.03070.08250.0305-0.0598-0.22460.01021.07570.87580.08760.9932-0.03880.56450.2967-47.7246-32.9161
44.6230.47321.4752.6991-0.20323.4020.372-0.7171-0.9412-0.1652-0.12880.00110.7143-0.9122-0.18690.97110.2397-0.11541.06630.19030.7701-19.4217-66.3337-13.9708
51.46930.0147-0.31190.98210.32912.3084-0.06510.3-0.0247-0.1801-0.1969-0.1142-0.29310.0115-0.08771.4820.78480.31771.07510.14840.4516.043-28.1797-44.5745
60.70660.4146-0.12860.6559-0.32910.18690.0856-0.196-0.23250.6208-0.2249-0.6507-0.35510.22260.18091.2127-0.1424-0.91850.48340.00541.730149.8293-82.7941-12.6671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'H' and (resid 2 through 111 )) or (chain 'L' and (resid 1 through 102 ))H0
2X-RAY DIFFRACTION2(chain 'H' and (resid 112 through 213)) or (chain 'L' and (resid 103 through 213 ))H0
3X-RAY DIFFRACTION3(chain 'A' and (resid 2 through 111 )) or (chain 'B' and (resid 1 through 102 ))A0
4X-RAY DIFFRACTION4(chain 'A' and (resid 112 through 213 )) or (chain 'B' and (resid 103 through 213 ))A0
5X-RAY DIFFRACTION5chain 'G' and (resid 305 through 404 )G305 - 404
6X-RAY DIFFRACTION6chain 'Z' and (resid 305 through 404 )Z305 - 404

+
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