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- PDB-6plk: Crystal structure of ZIKV-116 Fab in complex with ZIKV envelope DIII -

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Basic information

Entry
Database: PDB / ID: 6plk
TitleCrystal structure of ZIKV-116 Fab in complex with ZIKV envelope DIII
Components
  • Env
  • ZIKV-116 heavy chain
  • ZIKV-116 light chain
KeywordsANTIVIRAL PROTEIN / Human antibody / ZIKV-DIII / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / clathrin-dependent endocytosis of virus by host cell ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / molecular adaptor activity / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / centrosome / symbiont entry into host cell / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / 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 non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B ...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 non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical 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 / 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 / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Env
Similarity search - Component
Biological speciesHomo sapiens (human)
Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhao, H. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Exp.Med. / Year: 2020
Title: Mechanism of differential Zika and dengue virus neutralization by a public antibody lineage targeting the DIII lateral ridge.
Authors: Zhao, H. / Xu, L. / Bombardi, R. / Nargi, R. / Deng, Z. / Errico, J.M. / Nelson, C.A. / Dowd, K.A. / Pierson, T.C. / Crowe, J.E. / Diamond, M.S. / Fremont, D.H.
History
DepositionJul 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_volume / _citation.year ..._citation.journal_volume / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: ZIKV-116 heavy chain
L: ZIKV-116 light chain
E: Env
I: ZIKV-116 heavy chain
M: ZIKV-116 light chain
F: Env


Theoretical massNumber of molelcules
Total (without water)118,9506
Polymers118,9506
Non-polymers00
Water7,332407
1
H: ZIKV-116 heavy chain
L: ZIKV-116 light chain
E: Env


Theoretical massNumber of molelcules
Total (without water)59,4753
Polymers59,4753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-34 kcal/mol
Surface area24400 Å2
MethodPISA
2
I: ZIKV-116 heavy chain
M: ZIKV-116 light chain
F: Env


Theoretical massNumber of molelcules
Total (without water)59,4753
Polymers59,4753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-35 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.809, 89.805, 92.487
Angle α, β, γ (deg.)90.00, 103.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody ZIKV-116 heavy chain


Mass: 23990.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae gen. sp. (mammal)
#2: Antibody ZIKV-116 light chain


Mass: 23548.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae gen. sp. (mammal)
#3: Protein Env


Mass: 11935.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X9PPI0, UniProt: A0A024B7W1*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% MPD, 0.1 M Imidazole and 10% PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 50016 / % possible obs: 97.5 % / Redundancy: 6.5 % / Net I/σ(I): 22.5
Reflection shellResolution: 2.3→2.344 Å / Num. unique obs: 2471

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
REFMACrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KVG and 5GZO

5kvg

5gzo


Resolution: 2.3→44.903 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.8
RfactorNum. reflection% reflection
Rfree0.2107 2528 5.05 %
Rwork0.1674 --
obs0.1696 50016 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8232 0 0 407 8639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048432
X-RAY DIFFRACTIONf_angle_d0.65611476
X-RAY DIFFRACTIONf_dihedral_angle_d11.8595054
X-RAY DIFFRACTIONf_chiral_restr0.0451314
X-RAY DIFFRACTIONf_plane_restr0.0041450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.34430.29361210.25572350X-RAY DIFFRACTION87
2.3443-2.39210.27261480.23172616X-RAY DIFFRACTION98
2.3921-2.44410.26771110.22212695X-RAY DIFFRACTION98
2.4441-2.5010.30591390.21442631X-RAY DIFFRACTION98
2.501-2.56350.24091650.20442650X-RAY DIFFRACTION98
2.5635-2.63280.28631350.20252661X-RAY DIFFRACTION98
2.6328-2.71030.2671550.20452617X-RAY DIFFRACTION98
2.7103-2.79780.27641320.20912653X-RAY DIFFRACTION97
2.7978-2.89770.24371340.20262578X-RAY DIFFRACTION95
2.8977-3.01370.24121420.19892642X-RAY DIFFRACTION99
3.0137-3.15090.25361370.18592684X-RAY DIFFRACTION99
3.1509-3.31690.20171460.17552700X-RAY DIFFRACTION99
3.3169-3.52470.23231260.16952662X-RAY DIFFRACTION98
3.5247-3.79670.20951330.16142612X-RAY DIFFRACTION96
3.7967-4.17850.19391470.14982689X-RAY DIFFRACTION99
4.1785-4.78250.17931580.12632702X-RAY DIFFRACTION99
4.7825-6.02320.17341370.13952633X-RAY DIFFRACTION96
6.0232-44.9110.1531620.14042713X-RAY DIFFRACTION97

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