[English] 日本語
Yorodumi
- PDB-6dfi: Crystal structure of anti-Zika antibody Z021 bound to Zika virus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dfi
TitleCrystal structure of anti-Zika antibody Z021 bound to Zika virus envelope protein DIII
Components
  • Zika virus envelope protein DIII
  • anti-Zika antibody Z021, Heavy Chain
  • anti-Zika antibody Z021, Light Chain
KeywordsIMMUNE SYSTEM / antibody / Fab / Zika / Dengue / recurrent / neutralizing
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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
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 / 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 / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Core protein / Core protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Zika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsKeeffe, J.R. / Bjorkman, P.J.
CitationJournal: Cell Rep / Year: 2018
Title: A Combination of Two Human Monoclonal Antibodies Prevents Zika Virus Escape Mutations in Non-human Primates.
Authors: Keeffe, J.R. / Van Rompay, K.K.A. / Olsen, P.C. / Wang, Q. / Gazumyan, A. / Azzopardi, S.A. / Schaefer-Babajew, D. / Lee, Y.E. / Stuart, J.B. / Singapuri, A. / Watanabe, J. / Usachenko, J. / ...Authors: Keeffe, J.R. / Van Rompay, K.K.A. / Olsen, P.C. / Wang, Q. / Gazumyan, A. / Azzopardi, S.A. / Schaefer-Babajew, D. / Lee, Y.E. / Stuart, J.B. / Singapuri, A. / Watanabe, J. / Usachenko, J. / Ardeshir, A. / Saeed, M. / Agudelo, M. / Eisenreich, T. / Bournazos, S. / Oliveira, T.Y. / Rice, C.M. / Coffey, L.L. / MacDonald, M.R. / Bjorkman, P.J. / Nussenzweig, M.C. / Robbiani, D.F.
History
DepositionMay 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: anti-Zika antibody Z021, Heavy Chain
L: anti-Zika antibody Z021, Light Chain
E: Zika virus envelope protein DIII


Theoretical massNumber of molelcules
Total (without water)60,5393
Polymers60,5393
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-30 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.881, 105.622, 107.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Antibody anti-Zika antibody Z021, Heavy Chain


Mass: 24787.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293-6E / Production host: Homo sapiens (human)
#2: Antibody anti-Zika antibody Z021, Light Chain


Mass: 23815.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293-6E / Production host: Homo sapiens (human)
#3: Protein Zika virus envelope protein DIII


Mass: 11935.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Strain: Mr 766 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A172HA03, UniProt: A0A0U3FSM8*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES pH 7.0, 29% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.48→75.25 Å / Num. obs: 30524 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 44.52 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.077 / Net I/σ(I): 7.8
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3427 / CC1/2: 0.696 / Rpim(I) all: 0.418 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→75.25 Å / SU ML: 0.2876 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3011
RfactorNum. reflection% reflection
Rfree0.2285 1482 4.87 %
Rwork0.182 --
obs0.1842 30462 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.71 Å2
Refinement stepCycle: LAST / Resolution: 2.48→75.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 0 68 4163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784201
X-RAY DIFFRACTIONf_angle_d0.91025732
X-RAY DIFFRACTIONf_chiral_restr0.0526654
X-RAY DIFFRACTIONf_plane_restr0.0056729
X-RAY DIFFRACTIONf_dihedral_angle_d12.08422510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.560.3411330.26982618X-RAY DIFFRACTION99.96
2.56-2.650.26171340.2272584X-RAY DIFFRACTION100
2.65-2.750.24791270.20362614X-RAY DIFFRACTION99.85
2.75-2.880.21781310.18892548X-RAY DIFFRACTION98.13
2.88-3.030.22941280.18682619X-RAY DIFFRACTION99.96
3.03-3.220.19861330.1812632X-RAY DIFFRACTION99.93
3.22-3.470.22981410.17632603X-RAY DIFFRACTION99.82
3.47-3.820.22481420.17762626X-RAY DIFFRACTION99.35
3.82-4.370.23571660.17362620X-RAY DIFFRACTION99.93
4.37-5.510.21441340.16092684X-RAY DIFFRACTION99.61
5.51-75.290.21451130.18242832X-RAY DIFFRACTION99.33
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)
12.522965137420.794341302519-0.787243927742.11374830159-0.5333038982462.78543884320.002844868196210.1060716682410.005062256348740.03665720947290.1261484195010.189735173139-0.09698520132380.0602673720884-0.1142734709780.2449955065210.0455933514585-0.05596309008510.259501132047-0.03053994034160.237468088478-7.09540623026-23.70733079946.23173281379
23.622561306820.444859973062.226241619413.238118558590.2441856773986.10822134172-0.0654959817375-0.1156928590580.006138100386970.1872057308120.144779290067-0.28004347854-0.2007982778720.172927944011-0.08974539488680.253978323220.01628947622730.03199729932480.29320465419-0.03980593084160.27124180951122.0287866102-10.28462127364.04570982793
33.815790469942.546666296170.5839800809144.874752600170.7019829570642.387834813080.0356909841653-0.1924504915380.3311090762910.4271268365740.01411917953680.287888176182-0.223689192543-0.0269190024239-0.05212658868920.3455549246930.06055969336220.03518662712570.313946617758-0.04412688091220.2423354011-8.56332954134-8.4157086237822.2359827044
41.30515682124-0.338814036418-1.455744771622.305752191152.90946103977.92650168472-0.1025901572250.01547673561080.114521859603-0.281312458210.120516864313-0.135329387721-0.415600684767-0.140852559798-0.04089523648180.393820292284-0.0091759865534-0.003560255283520.309333097177-0.02215616440930.35944641562821.27391281845.478256088723.83836075294
51.02177081851.43172482227-0.5798287474165.81919766815-1.798827864353.123326452230.151250939004-0.07464368993720.0633293645652-0.00535373879818-0.04939006506320.6116226802350.0272073422787-0.221989806239-0.123197312770.2634592115880.0387653655121-0.01425765281930.3571174059160.03190580434740.38785473386-25.6916306832-39.105044615225.8888103828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'H' and resid 1 through 113)
2X-RAY DIFFRACTION2(chain 'H' and resid 114 through 215)
3X-RAY DIFFRACTION3(chain 'L' and resid 1 through 107)
4X-RAY DIFFRACTION4(chain 'L' and resid 108 through 213)
5X-RAY DIFFRACTION5(chain 'E' and resid 303 through 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