[English] 日本語
Yorodumi
- PDB-4jzo: Three dimensional structure of broadly neutralizing human anti - ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jzo
TitleThree dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC84-27
Components
  • Anti-HCV E2 Fab HC84-27 heavy chain
  • Anti-HCV E2 Fab HC84-27 light chain
  • Envelope glycoprotein E2
Keywordsimmune system/viral protein / Fab fragment / Immunglobulin fold / Antibody / immune system-viral protein complex
Function / homology
Function and homology information


positive regulation of hexokinase activity / symbiont-mediated perturbation of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / hepacivirin / TBC/RABGAPs / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / symbiont-mediated perturbation of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / hepacivirin / TBC/RABGAPs / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated transformation of host cell / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / endoplasmic reticulum-Golgi intermediate compartment membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / SH3 domain binding / kinase binding / nucleoside-triphosphate phosphatase / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase 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 / ribonucleoprotein complex / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : ...Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKrey, T. / Rey, F.A.
CitationJournal: Plos Pathog. / Year: 2013
Title: Structural basis of HCV neutralization by human monoclonal antibodies resistant to viral neutralization escape.
Authors: Krey, T. / Meola, A. / Keck, Z.Y. / Damier-Piolle, L. / Foung, S.K. / Rey, F.A.
History
DepositionApr 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Anti-HCV E2 Fab HC84-27 heavy chain
B: Anti-HCV E2 Fab HC84-27 light chain
C: Anti-HCV E2 Fab HC84-27 heavy chain
D: Anti-HCV E2 Fab HC84-27 heavy chain
E: Anti-HCV E2 Fab HC84-27 light chain
F: Anti-HCV E2 Fab HC84-27 light chain
G: Anti-HCV E2 Fab HC84-27 heavy chain
H: Anti-HCV E2 Fab HC84-27 light chain
I: Envelope glycoprotein E2
J: Envelope glycoprotein E2
K: Envelope glycoprotein E2
L: Envelope glycoprotein E2


Theoretical massNumber of molelcules
Total (without water)209,72412
Polymers209,72412
Non-polymers00
Water5,423301
1
A: Anti-HCV E2 Fab HC84-27 heavy chain
B: Anti-HCV E2 Fab HC84-27 light chain
J: Envelope glycoprotein E2


Theoretical massNumber of molelcules
Total (without water)52,4313
Polymers52,4313
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-32 kcal/mol
Surface area19570 Å2
MethodPISA
2
C: Anti-HCV E2 Fab HC84-27 heavy chain
F: Anti-HCV E2 Fab HC84-27 light chain
K: Envelope glycoprotein E2


Theoretical massNumber of molelcules
Total (without water)52,4313
Polymers52,4313
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-32 kcal/mol
Surface area19210 Å2
MethodPISA
3
D: Anti-HCV E2 Fab HC84-27 heavy chain
E: Anti-HCV E2 Fab HC84-27 light chain
I: Envelope glycoprotein E2


Theoretical massNumber of molelcules
Total (without water)52,4313
Polymers52,4313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-32 kcal/mol
Surface area19470 Å2
MethodPISA
4
G: Anti-HCV E2 Fab HC84-27 heavy chain
H: Anti-HCV E2 Fab HC84-27 light chain
L: Envelope glycoprotein E2


Theoretical massNumber of molelcules
Total (without water)52,4313
Polymers52,4313
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-34 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.940, 77.330, 85.820
Angle α, β, γ (deg.)92.10, 107.62, 90.24
Int Tables number1
Space group name H-MP1
DetailsThe asymetric unit contains four Fab molecules each representing a heterodimer of heavy and light chain. Each Fab molecule binds one synthetic peptide.

-
Components

#1: Antibody
Anti-HCV E2 Fab HC84-27 heavy chain


Mass: 27553.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT Fab / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody
Anti-HCV E2 Fab HC84-27 light chain


Mass: 23340.764 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT Fab / Production host: Drosophila melanogaster (fruit fly)
#3: Protein/peptide
Envelope glycoprotein E2 / NS1 / gp68 / gp70 / Genome polyprotein


Mass: 1536.732 Da / Num. of mol.: 4 / Fragment: Residues 434-446 of HCV strain H77 polyprotein / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus (isolate H)
References: UniProt: P27958, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase, RNA-directed RNA polymerase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 23% PEG 3350 250mM Sodium Thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2012
RadiationMonochromator: LN2 cooled Fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.22→41.35 Å / Num. all: 91860 / Num. obs: 78908 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.6 % / Biso Wilson estimate: 41.25 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.3
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 2 / % possible all: 71

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XZA and 3QOT

2xza

3qot
PDB Unreleased entry


Resolution: 2.22→41.35 Å / Cor.coef. Fo:Fc: 0.9248 / Cor.coef. Fo:Fc free: 0.9059 / SU R Cruickshank DPI: 0.338 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 3996 5.07 %RANDOM
Rwork0.1955 ---
obs0.1976 78809 85.79 %-
all-91745 --
Displacement parametersBiso mean: 40.42 Å2
Baniso -1Baniso -2Baniso -3
1-6.9646 Å2-0.9709 Å2-0.7298 Å2
2--5.193 Å2-0.7857 Å2
3----12.1577 Å2
Refine analyzeLuzzati coordinate error obs: 0.283 Å
Refinement stepCycle: LAST / Resolution: 2.22→41.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13189 0 0 301 13490
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113594HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1818551HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4461SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes282HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2006HARMONIC5
X-RAY DIFFRACTIONt_it13594HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion18.19
X-RAY DIFFRACTIONt_chiral_improper_torsion1804SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_utility_distance7HARMONIC1
X-RAY DIFFRACTIONt_utility_angle14HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact14455SEMIHARMONIC4
LS refinement shellResolution: 2.22→2.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 220 4.75 %
Rwork0.2238 4414 -
all0.2261 4634 -
obs--85.79 %

+
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