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- PDB-5kzp: Structure of the HCV1-C1 Antibody-Antigen Complex -

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Basic information

Entry
Database: PDB / ID: 5kzp
TitleStructure of the HCV1-C1 Antibody-Antigen Complex
Components
  • (HCV1-C1 Antibody Fab ...) x 2
  • C1 Epitope
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / Antigen / HCV / Vaccine / Virology / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / SH3 domain binding / : ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / SH3 domain 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 / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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 / 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
ACETATE ION / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.262 Å
AuthorsPiepenbrink, K.H. / Sundberg, E.J.
CitationJournal: J. Virol. / Year: 2017
Title: Structure-Based Design of Hepatitis C Virus Vaccines That Elicit Neutralizing Antibody Responses to a Conserved Epitope.
Authors: Pierce, B.G. / Boucher, E.N. / Piepenbrink, K.H. / Ejemel, M. / Rapp, C.A. / Thomas, W.D. / Sundberg, E.J. / Weng, Z. / Wang, Y.
History
DepositionJul 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: 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 1.2Oct 11, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: HCV1-C1 Antibody Fab Heavy Chain
L: HCV1-C1 Antibody Fab Light Chain
A: C1 Epitope
E: HCV1-C1 Antibody Fab Heavy Chain
I: HCV1-C1 Antibody Fab Light Chain
B: C1 Epitope
F: HCV1-C1 Antibody Fab Heavy Chain
J: HCV1-C1 Antibody Fab Light Chain
C: C1 Epitope
G: HCV1-C1 Antibody Fab Heavy Chain
K: HCV1-C1 Antibody Fab Light Chain
D: C1 Epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,91637
Polymers198,83812
Non-polymers1,07825
Water9,872548
1
H: HCV1-C1 Antibody Fab Heavy Chain
L: HCV1-C1 Antibody Fab Light Chain
A: C1 Epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9699
Polymers49,7103
Non-polymers2596
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-76 kcal/mol
Surface area20600 Å2
MethodPISA
2
E: HCV1-C1 Antibody Fab Heavy Chain
I: HCV1-C1 Antibody Fab Light Chain
B: C1 Epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8496
Polymers49,7103
Non-polymers1393
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-50 kcal/mol
Surface area20780 Å2
MethodPISA
3
F: HCV1-C1 Antibody Fab Heavy Chain
J: HCV1-C1 Antibody Fab Light Chain
C: C1 Epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,04911
Polymers49,7103
Non-polymers3408
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-96 kcal/mol
Surface area20530 Å2
MethodPISA
4
G: HCV1-C1 Antibody Fab Heavy Chain
K: HCV1-C1 Antibody Fab Light Chain
D: C1 Epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,04911
Polymers49,7103
Non-polymers3408
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-100 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.070, 94.538, 126.758
Angle α, β, γ (deg.)91.84, 94.95, 97.91
Int Tables number1
Space group name H-MP1

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Components

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Protein/peptide , 1 types, 4 molecules ABCD

#3: Protein/peptide
C1 Epitope


Mass: 1732.981 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: P26663*PLUS

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Antibody , 2 types, 8 molecules HEFGLIJK

#1: Antibody
HCV1-C1 Antibody Fab Heavy Chain


Mass: 24580.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: B-Lymphocyte / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody
HCV1-C1 Antibody Fab Light Chain


Mass: 23395.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 573 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 0.1M MES pH 6.0 0.2M Calcium Acetate 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.26→29.49 Å / Num. obs: 186500 / % possible obs: 92.66 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.4

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Processing

Software
NameVersionClassification
PHENIX1.10pre_2124refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.262→29.49 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.65
RfactorNum. reflection% reflection
Rfree0.2611 9022 4.84 %
Rwork0.2181 --
obs0.2202 186455 92.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.262→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13921 0 37 548 14506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01214403
X-RAY DIFFRACTIONf_angle_d1.58719626
X-RAY DIFFRACTIONf_dihedral_angle_d17.5998634
X-RAY DIFFRACTIONf_chiral_restr0.0982200
X-RAY DIFFRACTIONf_plane_restr0.012522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2616-2.28730.36832070.33493794X-RAY DIFFRACTION61
2.2873-2.31420.32572670.31065609X-RAY DIFFRACTION87
2.3142-2.34240.34582960.29586089X-RAY DIFFRACTION95
2.3424-2.3720.31982710.30446058X-RAY DIFFRACTION95
2.372-2.40320.35232810.29635962X-RAY DIFFRACTION95
2.4032-2.43610.33933190.29996187X-RAY DIFFRACTION95
2.4361-2.47090.3463260.30496110X-RAY DIFFRACTION95
2.4709-2.50780.34322990.29325914X-RAY DIFFRACTION95
2.5078-2.5470.32353360.28196055X-RAY DIFFRACTION95
2.547-2.58870.31273600.27326077X-RAY DIFFRACTION95
2.5887-2.63330.29423200.26856099X-RAY DIFFRACTION95
2.6333-2.68120.29912950.24496058X-RAY DIFFRACTION95
2.6812-2.73270.27433060.2356050X-RAY DIFFRACTION95
2.7327-2.78840.27223810.22915998X-RAY DIFFRACTION95
2.7884-2.8490.30992760.23945970X-RAY DIFFRACTION94
2.849-2.91520.30252830.24926095X-RAY DIFFRACTION94
2.9152-2.98810.3062890.24176031X-RAY DIFFRACTION95
2.9881-3.06880.31833290.22175977X-RAY DIFFRACTION94
3.0688-3.1590.262860.2156194X-RAY DIFFRACTION94
3.159-3.26080.22442650.22255997X-RAY DIFFRACTION95
3.2608-3.37720.28673370.21526039X-RAY DIFFRACTION94
3.3772-3.51220.25162770.21035886X-RAY DIFFRACTION93
3.5122-3.67180.24793210.19816000X-RAY DIFFRACTION93
3.6718-3.8650.23422790.19335945X-RAY DIFFRACTION93
3.865-4.10650.24093030.19555874X-RAY DIFFRACTION92
4.1065-4.42260.25052900.18325803X-RAY DIFFRACTION91
4.4226-4.86590.20193000.17385890X-RAY DIFFRACTION92
4.8659-5.56590.19833270.1815868X-RAY DIFFRACTION92
5.5659-6.9970.26232880.20425878X-RAY DIFFRACTION92
6.997-29.49440.23413080.20785926X-RAY DIFFRACTION93
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)
11.9943-0.0649-0.12591.78770.28452.5269-0.059-0.2685-0.25240.1430.08260.05090.25590.0609-0.0940.20340.0258-0.02560.31520.11530.3384-4.2496-9.291328.0109
22.47550.0852-0.29182.58920.82682.0697-0.4293-1.011-0.08881.20870.32740.49080.0012-0.003-0.04370.73370.12470.14340.85720.06910.3864-20.42557.214557.7262
32.2262-0.5431-0.18571.86750.16721.3363-0.1101-0.1022-0.08840.01350.10930.2670.0271-0.23140.04870.1959-0.0137-0.06580.36220.10070.3351-20.74784.310620.9911
41.5051-0.2965-0.43491.85820.44051.7694-0.2569-0.47070.6870.40270.2261-0.1599-1.00440.08690.01490.8492-0.018-0.07640.6365-0.14010.5824-19.727321.33351.2644
52.04510.49290.57722.51172.70923.0423-0.00240.07150.4-0.57950.205-0.3129-0.23660.2204-0.12210.2833-0.03260.03180.33260.03910.44221.1269-8.34189.8189
61.65041.04290.54762.32410.4730.5273-0.66780.28660.8636-2.40680.39111.3176-0.4248-0.16160.01881.3849-0.1733-0.51470.33720.25940.6365-9.5623-22.8053-14.4385
71.8053-0.902-0.24912.32731.23840.71420.13660.4802-0.8176-0.49450.07910.93240.1007-0.23840.51482.7644-0.3556-0.43810.7488-0.15311.0634-13.8977-51.7316-37.088
81.383-0.140.06991.8253-0.53561.5032-0.11830.2818-0.2816-1.040.1761-0.19390.22230.0641-0.04650.6146-0.09030.04280.3331-0.00590.4270.2778-42.1554-10.3578
91.4291-0.5763-0.91140.26580.60081.96360.24110.5222-0.4501-1.15820.3428-0.16830.45341.253-0.14342.2235-0.09440.19741.2513-0.43760.90252.5032-55.1014-35.3344
102.42321.52830.28261.44390.69480.6277-0.2926-0.16460.6388-0.76580.4858-0.2138-0.54510.43830.08640.4658-0.0521-0.03390.32910.01530.4280.478-12.9392-1.4052
112.7330.9263-0.59322.8439-0.04191.1216-0.08390.06040.5122-0.20610.13710.42810.0407-0.2553-0.05190.1986-0.027-0.0440.29630.02680.4042-1.935526.675310.5303
120.4073-0.2729-0.37781.1179-0.4152.0527-0.0967-0.7451.20950.5561-0.52410.6017-0.8472-0.20990.03120.82170.01240.18960.8825-0.71981.8905-0.922957.08132.0184
133.01021.1104-0.22591.6382-0.35231.4570.0664-0.54060.26420.1407-0.11950.0626-0.12320.1136-0.01280.18760.00690.00690.3285-0.00630.381417.400635.518317.5157
141.07140.02950.59260.65650.33040.5666-0.1578-1.15150.14590.9341-0.12180.2001-0.11870.55280.18531.0432-0.05310.21041.3925-0.43290.966911.111750.004941.3095
151.35220.00810.70412.3715-0.94742.9290.12380.0952-0.7104-0.68470.2763-0.89280.6290.0001-0.11060.5832-0.14550.11550.3354-0.02750.49866.40110.34235.0329
163.6980.79390.68171.04450.39071.59680.69810.37690.50230.6054-0.3015-0.05981.48420.8920.08931.14580.38410.04290.59070.12760.200320.19923.381-21.2213
172.9779-1.3008-1.52314.66561.14362.23970.10030.63420.1574-0.5430.2611-0.2773-0.0228-0.08-0.30020.46530.10910.03090.8059-0.0080.362521.1219-6.4035-57.4812
181.993-0.22211.2161.28711.22332.25030.08310.2103-0.02530.9553-0.95990.7371.098-0.8880.23760.7055-0.15570.3340.5868-0.18110.5619-0.81223.746-29.7573
191.6974-0.2521-0.23511.71591.1152.417-0.10491.3145-1.62410.1767-0.78191.0980.7282-0.66280.40530.5091-0.01980.09330.9491-0.51861.06989.3407-16.3574-56.15
203.9350.409-0.3410.70820.18270.10090.3828-0.4110.19020.3308-0.3868-0.20230.8271-0.2124-0.38491.3685-0.03990.28740.1780.00190.410910.84153.7398-4.7254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 121 )
2X-RAY DIFFRACTION2chain 'H' and (resid 122 through 226 )
3X-RAY DIFFRACTION3chain 'L' and (resid 1 through 113 )
4X-RAY DIFFRACTION4chain 'L' and (resid 114 through 213 )
5X-RAY DIFFRACTION5chain 'A' and (resid 411 through 425 )
6X-RAY DIFFRACTION6chain 'E' and (resid 1 through 121 )
7X-RAY DIFFRACTION7chain 'E' and (resid 122 through 226 )
8X-RAY DIFFRACTION8chain 'I' and (resid 1 through 128 )
9X-RAY DIFFRACTION9chain 'I' and (resid 129 through 213 )
10X-RAY DIFFRACTION10chain 'B' and (resid 411 through 425)
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 121)
12X-RAY DIFFRACTION12chain 'F' and (resid 122 through 226)
13X-RAY DIFFRACTION13chain 'J' and (resid 1 through 128)
14X-RAY DIFFRACTION14chain 'J' and (resid 129 through 213)
15X-RAY DIFFRACTION15chain 'C' and (resid 411 through 425)
16X-RAY DIFFRACTION16chain 'G' and (resid 1 through 121 )
17X-RAY DIFFRACTION17chain 'G' and (resid 122 through 226 )
18X-RAY DIFFRACTION18chain 'K' and (resid 1 through 113)
19X-RAY DIFFRACTION19chain 'K' and (resid 114 through 212)
20X-RAY DIFFRACTION20chain 'D' and (resid 411 through 425)

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