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- PDB-4hzl: Neutralizing antibody mAb#8 in complex with the Epitope II of HCV... -

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Basic information

Entry
Database: PDB / ID: 4hzl
TitleNeutralizing antibody mAb#8 in complex with the Epitope II of HCV E2 envelope protein
Components
  • E2 envelop protein
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / Ig domain / neutralizing antibody
Function / homology
Function and homology information


hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / modulation by virus of host G1/S transition checkpoint / transformation of host cell by virus / lipid droplet / suppression by virus of host JAK-STAT cascade via inhibition of STAT1 activity / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / host cell endoplasmic reticulum membrane / integral to membrane of host cell ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / modulation by virus of host G1/S transition checkpoint / transformation of host cell by virus / lipid droplet / suppression by virus of host JAK-STAT cascade via inhibition of STAT1 activity / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / host cell endoplasmic reticulum membrane / integral to membrane of host cell / pore formation by virus in membrane of host cell / suppression by virus of host TRAF activity / protein complex oligomerization / nucleoside-triphosphate phosphatase / ion channel activity / host cell perinuclear region of cytoplasm / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / RNA helicase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / suppression by virus of host type I interferon-mediated signaling pathway / virion attachment to host cell / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / serine-type endopeptidase activity / host cell plasma membrane / virion membrane / endoplasmic reticulum membrane / structural molecule activity / RNA binding / zinc ion binding / integral component of membrane / extracellular region / ATP binding / plasma membrane / nucleus
Similarity search - Function
Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus NS5A, 1B domain superfamily / HCV NS5a protein C-terminal region / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitus C virus, NS5a, C-terminal / Hepatitis C virus capsid protein / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus core protein, N-terminal / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus non-structural protein NS2 ...Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus NS5A, 1B domain superfamily / HCV NS5a protein C-terminal region / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitus C virus, NS5a, C-terminal / Hepatitis C virus capsid protein / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus core protein, N-terminal / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus non-structural protein NS2 / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a protein / Hepatitis C virus non-structural protein NS2 / Hepatitis C virus non-structural 5a protein membrane anchor / NS5A domain 1a / Hepatitis C virus non-structural 5a, 1B domain / Hepatitis C virus non-structural 5a domain 1b / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / NS5A domain 1a superfamily / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus core protein / Hepatitis C virus core protein, C-terminal / 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 / Peptidase S29, hepatitis C virus NS3 protease / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / Viral RNA dependent RNA polymerase / RNA dependent RNA polymerase, hepatitis C virus / Flavivirus DEAD domain / DEAD box, Flavivirus / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Helicase, C-terminal / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, catalytic domain / Reverse transcriptase/Diguanylate cyclase domain / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Immunoglobulins / Immunoglobulin-like / P-loop containing nucleoside triphosphate hydrolase / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Recombinant Hepatitis C virus H77/JFH1_V787A
Q1247L
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsDeng, L. / Zhang, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural evidence for a bifurcated mode of action in the antibody-mediated neutralization of hepatitis C virus.
Authors: Deng, L. / Zhong, L. / Struble, E. / Duan, H. / Ma, L. / Harman, C. / Yan, H. / Virata-Theimer, M.L. / Zhao, Z. / Feinstone, S. / Alter, H. / Zhang, P.
History
DepositionNov 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
E: E2 envelop protein
A: Fab heavy chain
B: Fab light chain
F: E2 envelop protein


Theoretical massNumber of molelcules
Total (without water)99,2196
Polymers99,2196
Non-polymers00
Water2,288127
1
H: Fab heavy chain
L: Fab light chain
E: E2 envelop protein


Theoretical massNumber of molelcules
Total (without water)49,6093
Polymers49,6093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-35 kcal/mol
Surface area19520 Å2
MethodPISA
2
A: Fab heavy chain
B: Fab light chain
F: E2 envelop protein


Theoretical massNumber of molelcules
Total (without water)49,6093
Polymers49,6093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-35 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)137.252, 137.252, 140.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21H
12A
22H
13B
23L
14B
24L
15F
25E
/ NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.503337, -0.081173, -0.860269), (0.146175, -0.989228, 0.007815), (-0.851636, -0.121816, 0.509781)-66.30408, 97.60838, -34.91712
DetailsProtein molecule complex contains Fab fragments of an IgG antibody in complex with a peptide antigen

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Components

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


Mass: 23744.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab light chain / Fragment antigen-binding


Mass: 23884.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide E2 envelop protein


Mass: 1980.184 Da / Num. of mol.: 2 / Fragment: Epitope II residues 430-446 / Source method: isolated from a natural source
Source: (natural) Recombinant Hepatitis C virus H77(5'UTR-NS2)/JFH1_V787A,Q1247L
Strain: H77 / References: UniProt: F5BWY6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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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: 3.33 Å3/Da / Density % sol: 63.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl buffer (pH 8.0) 16% (wt/vol) polyethylene glycol 10,000, 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 30296 / % possible obs: 99.8 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 10.8
Reflection shellResolution: 2.85→3 Å / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.8 / % possible all: 53.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZEA
Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.836 / SU B: 32.53 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R: 1.07 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27715 1636 5.1 %RANDOM
Rwork0.22094 ---
obs0.22387 30296 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.489 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å2-0 Å2
2---0.96 Å2-0 Å2
3---1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6822 0 0 127 6949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026998
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.9589542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4425886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61223.985266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.453151106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8711530
X-RAY DIFFRACTIONr_chiral_restr0.1310.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215258
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A8443.36
2A6493.06
3B2945.61
4B9607.21
5F10014.14
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 104 -
Rwork0.362 2015 -
obs--99.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.88970.67480.64870.83460.39852.6130.2049-0.1250.06660.1051-0.10110.0484-0.031-0.1841-0.10370.0586-0.0172-0.01210.03740.0180.0444-66.71225.4651-20.1905
22.3080.2946-0.77042.6160.22741.56420.0607-0.176-0.10580.1907-0.1118-0.1264-0.0840.24740.05110.059-0.0426-0.04690.05650.03080.0928-34.07330.3867-7.4435
33.57011.25890.01052.96390.6631.20480.4586-0.6263-0.21050.8477-0.53410.10860.3432-0.25680.07550.3501-0.2705-0.00210.25420.03520.0844-17.455462.46198.5206
43.95920.1493-0.41232.71220.90832.43740.3236-0.19110.6309-0.06430.0289-0.0314-0.2396-0.0452-0.35250.1358-0.05920.1850.0435-0.06360.3231-46.580959.3641-12.828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 120
2X-RAY DIFFRACTION1L1 - 110
3X-RAY DIFFRACTION2H129 - 222
4X-RAY DIFFRACTION2L119 - 217
5X-RAY DIFFRACTION3A1 - 120
6X-RAY DIFFRACTION3B1 - 110
7X-RAY DIFFRACTION4A129 - 222
8X-RAY DIFFRACTION4B119 - 217

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