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- PDB-5fgb: Three dimensional structure of broadly neutralizing human anti - ... -

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Basic information

Entry
Database: PDB / ID: 5fgb
TitleThree dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC33.4
Components
  • (Anti-HCV E2 Fab HC84-1 ...) x 2
  • Genome polyprotein
KeywordsIMMUNE SYSTEM / Fab fragment / neutralizing antibody / Hepatitis C virus E2
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 transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / 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 / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Hepatitis C virus genotype 1a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGirard-Blanc, C. / Rey, F.A. / Krey, T.
Funding support France, 1items
OrganizationGrant numberCountry
ANRS France
CitationJournal: J.Virol. / Year: 2016
Title: Antibody Response to Hypervariable Region 1 Interferes with Broadly Neutralizing Antibodies to Hepatitis C Virus.
Authors: Keck, Z.Y. / Girard-Blanc, C. / Wang, W. / Lau, P. / Zuiani, A. / Rey, F.A. / Krey, T. / Diamond, M.S. / Foung, S.K.
History
DepositionDec 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-HCV E2 Fab HC84-1 light chain
B: Anti-HCV E2 Fab HC84-1 light chain
C: Anti-HCV E2 Fab HC84-1 heavy chain
E: Anti-HCV E2 Fab HC84-1 heavy chain
F: Genome polyprotein
G: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,43017
Polymers108,3906
Non-polymers1,04111
Water10,881604
1
A: Anti-HCV E2 Fab HC84-1 light chain
C: Anti-HCV E2 Fab HC84-1 heavy chain
F: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,85910
Polymers54,1953
Non-polymers6657
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-68 kcal/mol
Surface area19560 Å2
MethodPISA
2
B: Anti-HCV E2 Fab HC84-1 light chain
E: Anti-HCV E2 Fab HC84-1 heavy chain
G: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5717
Polymers54,1953
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-52 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.810, 149.430, 67.950
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 2 molecules FG

#3: Protein/peptide Genome polyprotein


Mass: 2295.511 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Fragment Residues 406-425 of HCV strain H77 polyprotein
Source: (synth.) Hepatitis C virus genotype 1a (isolate H)
References: UniProt: P27958, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase, RNA-directed RNA polymerase

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Antibody , 2 types, 4 molecules ABCE

#1: Antibody Anti-HCV E2 Fab HC84-1 light chain


Mass: 23509.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT/BiP modified / Cell line (production host): Schneider 2 / Production host: Drosophila (fruit flies)
#2: Antibody Anti-HCV E2 Fab HC84-1 heavy chain


Mass: 28389.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT/BiP modified / Cell line (production host): Schneider 2 / Production host: Drosophila (fruit flies)

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Non-polymers , 3 types, 615 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 100 mM sodium citrate pH 5.2 300 mM ammonium sulfate 100 mM potassium phosphate 1 M lithium chloride

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 118795 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 23.98 Å2 / Net I/σ(I): 12.52
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.63 / % possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: hypthetical Fab assembled from the light chain of PDB 4JZO and the heavy chain of PDB 3KDM

4jzo

3kdm


Resolution: 1.65→24.16 Å / Cor.coef. Fo:Fc: 0.9536 / Cor.coef. Fo:Fc free: 0.9514 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.081 / SU Rfree Blow DPI: 0.077 / SU Rfree Cruickshank DPI: 0.077
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 5936 5 %RANDOM
Rwork0.1711 ---
obs0.172 118727 99.91 %-
Displacement parametersBiso mean: 29.36 Å2
Baniso -1Baniso -2Baniso -3
1-3.2049 Å20 Å21.1656 Å2
2--4.792 Å20 Å2
3----7.9969 Å2
Refine analyzeLuzzati coordinate error obs: 0.194 Å
Refinement stepCycle: 1 / Resolution: 1.65→24.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6589 0 59 604 7252
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016811HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.099298HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2251SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1015HARMONIC5
X-RAY DIFFRACTIONt_it6811HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.24
X-RAY DIFFRACTIONt_other_torsion14.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion903SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance12HARMONIC1
X-RAY DIFFRACTIONt_utility_angle12HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7872SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2516 434 4.99 %
Rwork0.2343 8255 -
all0.2352 8689 -
obs--99.91 %
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)
11.4818-0.91661.51451.1706-1.49263.2122-0.01770.0794-0.11510.06140.0113-0.1-0.02690.09940.0064-0.0584-0.00710.019-0.034-0.0107-0.0179-19.281226.875343.8978
21.12720.01410.27191.9649-0.40150.4469-0.00820.0037-0.01110.02620.0860.0068-0.1274-0.0667-0.0778-0.0084-0.00440.0028-0.03490.0015-0.0062-27.411233.440643.4052
31.7788-0.35080.89211.2188-0.66831.2709-0.00250.0083-0.03910.08360.10720.1675-0.095-0.0367-0.1047-0.045-0.00060.0058-0.05330.0132-0.0108-28.926.718146.7267
40.81940.18340.15831.79180.2650.8005-0.00690.058-0.0244-0.1278-0.03740.00570.07050.01350.0443-0.0108-0.0039-0.01050.01650.0062-0.0312-16.07932.120948.0129
51.67380.0642-0.27980.28430.5341.307-0.01190.0757-0.0737-0.0595-0.00260.00160.09110.20440.0146-0.02450.02310.00440.01090.01390.0158-9.0226-3.050244.2525
63.163-1.23920.50922.6339-1.11370.99750.0824-0.0691-0.3168-0.04690.08520.30340.0763-0.0953-0.1677-0.1245-0.0048-0.0204-0.07290.04170.0035-45.6353-7.848523.3598
73.5173-0.86430.65230.90930.13171.88220.16310.1436-0.5429-0.2240.09440.03780.3773-0.0856-0.25750.0018-0.0017-0.0694-0.0118-0.00680.0828-40.3555-13.246418.1684
81.69820.3355-0.19441.4475-0.37510.4980.04450.08740.07370.0079-0.010.108-0.02270.0034-0.0345-0.0550.0085-0.0028-0.00850.0069-0.0208-22.349815.737513.5685
91.0034-0.65940.44432.0194-0.33232.0614-0.03510.20050.1907-0.27760.05260.2097-0.08890.1143-0.0176-0.0237-0.0053-0.0037-0.01340.0392-0.05-17.112415.85252.2495
103.35760.7962-1.16841.3442-0.61751.27910.00940.16530.1944-0.0779-0.00390.0871-0.08550.0161-0.0055-0.0529-0.0008-0.0113-0.01380.0181-0.0173-20.978417.570110.428
111.6546-0.1835-0.19891.3568-0.19650.43670.0521-0.0654-0.0547-0.01980.04570.14680.098-0.0343-0.0978-0.03480.0022-0.0225-0.05630.0096-0.0072-26.6291-20.039227.5355
121.33710.2285-0.51112.92921.10221.89780.0035-0.1242-0.1186-0.00440.0785-0.0760.15670.0188-0.082-0.01410.0158-0.0206-0.02630.00010.0252-22.8586-25.456529.7485
130.46930.38250.05481.1539-0.56050.48540.03380.0221-0.0025-0.07530.06420.14520.0878-0.019-0.098-0.03060.0109-0.001-0.0279-0.00180.0043-23.8688-11.325823.4094
140.8620.20650.1781.4774-0.16540.72970.0006-0.0476-0.0120.1059-0.06580.1138-0.087-0.05480.0652-0.10020.01180.0072-0.0802-0.0006-0.1104-17.84876.994321.3969
150.7573-1.1461-0.49923.4540.85870.112-0.009-0.10540.1770.2948-0.0155-0.3699-0.05720.10170.02440.0512-0.0018-0.01340.0179-0.00080.0206-12.897211.30728.9811
162.1451.3961-0.47273.1633-1.45881.03390.07560.06550.24030.15650.16050.4895-0.1114-0.1364-0.2361-0.10730.01640.0323-0.0450.05690.042-44.931418.983348.9382
173.4789-0.2240.17061.6208-0.35550.54150.08380.0318-0.1208-0.0147-0.04210.04650.04840.0409-0.0417-0.0688-0.00170-0.02380.0101-0.0691-20.8524-5.390356.7057
181.52730.0448-0.16220.55510.17892.091-0.0463-0.2-0.14830.22280.0360.21260.0546-0.0240.0102-0.01080.0061-0.0062-0.00550.0372-0.0243-19.8929-5.547468.9299
193.2673-0.730.97781.1828-0.70181.0059-0.0490.01580.12240.0572-0.02540.0451-0.00570.07220.0745-0.0540.0015-0.01060.00760.0094-0.0168-22.7884-0.787557.6471
205.9726-0.67542.01832.3262-1.09281.70070.0551-0.3459-0.54710.07050.01350.0680.1994-0.008-0.0686-0.03940.0026-0.0012-0.02180.04610.0029-18.8804-12.806764.1249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{C|1 - 20}
2X-RAY DIFFRACTION2{C|21 - 86}
3X-RAY DIFFRACTION3{C|87 - 126}
4X-RAY DIFFRACTION4{C|127 - 214}
5X-RAY DIFFRACTION5{C|215 - 223}
6X-RAY DIFFRACTION6{B|1 - 90}
7X-RAY DIFFRACTION7{B|91 - 106}
8X-RAY DIFFRACTION8{B|107 - 147}
9X-RAY DIFFRACTION9{B|148 - 161}
10X-RAY DIFFRACTION10{B|162 - 212}
11X-RAY DIFFRACTION11{E|1 - 64}
12X-RAY DIFFRACTION12{E|65 - 83}
13X-RAY DIFFRACTION13{E|84 - 135}
14X-RAY DIFFRACTION14{E|143 - 193}
15X-RAY DIFFRACTION15{E|194 - 222}
16X-RAY DIFFRACTION16{A|1 - 107}
17X-RAY DIFFRACTION17{A|108 - 142}
18X-RAY DIFFRACTION18{A|143 - 160}
19X-RAY DIFFRACTION19{A|161 - 186}
20X-RAY DIFFRACTION20{A|187 - 213}

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