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- PDB-4jzo: Three dimensional structure of broadly neutralizing human anti - ... -

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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 / modulation by virus 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 / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus 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 / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endoplasmic reticulum-Golgi intermediate compartment membrane / SH3 domain binding / kinase binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / entry receptor-mediated virion attachment to host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / ribonucleoprotein complex / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
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 non-structural protein NS4b ...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 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 / 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. / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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 / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 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

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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

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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 %

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