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- PDB-6cvk: Hepatitis B e-antigen in complex with scFv e13 -

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Basic information

Entry
Database: PDB / ID: 6cvk
TitleHepatitis B e-antigen in complex with scFv e13
Components
  • Capsid proteinCapsid
  • Single chain variable fragment (scFv) e13
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HEPATITIS B / SINGLE CHAIN VARIABLE FRAGMENT / E-ANTIGEN / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / : / virus-mediated perturbation of host defense response / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding ...virus-mediated perturbation of host defense response => GO:0019049 / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / : / virus-mediated perturbation of host defense response / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / extracellular region
Similarity search - Function
Hepatitis B viral capsid (hbcag) fold / Viral capsid, core domain supefamily, Hepatitis B virus / Hepatitis B virus, capsid N-terminal / Hepatitis core protein, putative zinc finger / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Capsid protein / Capsid protein
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Hepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsEren, E. / Steven, A.C. / Wingfield, P.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)Intramural Research Program United States
CitationJournal: Structure / Year: 2018
Title: Structures of Hepatitis B Virus Core- and e-Antigen Immune Complexes Suggest Multi-point Inhibition.
Authors: Eren, E. / Watts, N.R. / Dearborn, A.D. / Palmer, I.W. / Kaufman, J.D. / Steven, A.C. / Wingfield, P.T.
History
DepositionMar 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
B: Single chain variable fragment (scFv) e13
A: Single chain variable fragment (scFv) e13
C: Capsid protein
D: Capsid protein


Theoretical massNumber of molelcules
Total (without water)89,3524
Polymers89,3524
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-25 kcal/mol
Surface area34390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.490, 192.140, 64.980
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Single chain variable fragment (scFv) e13


Mass: 26810.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Escherichia coli (E. coli)
#2: Protein Capsid protein / Capsid / Core antigen / Core protein / HBcAg / p21.5


Mass: 17865.424 Da / Num. of mol.: 2 / Mutation: C58A, C117A, E74D, M103V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Gene: C, preC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QMH8, UniProt: L7R8Z1*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 3.41 Å3/Da / Density % sol: 63.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 15% (w/v) PEG 550 MME, 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→20 Å / Num. obs: 44849 / % possible obs: 100 % / Redundancy: 5.1 % / CC1/2: 0.99 / Rpim(I) all: 0.072 / Rrim(I) all: 0.16 / Net I/σ(I): 10.3
Reflection shellResolution: 2.38→2.48 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4459 / CC1/2: 0.59 / Rpim(I) all: 0.58 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V6Z, 2KH2

3v6z

2kh2


Resolution: 2.38→19.785 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2209 3956 4.45 %
Rwork0.1748 --
obs0.1768 88848 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→19.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5884 0 0 266 6150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126052
X-RAY DIFFRACTIONf_angle_d1.3128275
X-RAY DIFFRACTIONf_dihedral_angle_d13.4863529
X-RAY DIFFRACTIONf_chiral_restr0.07952
X-RAY DIFFRACTIONf_plane_restr0.011043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.4090.28521400.29022984X-RAY DIFFRACTION100
2.409-2.43940.34371390.2893051X-RAY DIFFRACTION100
2.4394-2.47150.3311400.28363042X-RAY DIFFRACTION100
2.4715-2.50530.37251430.28483015X-RAY DIFFRACTION100
2.5053-2.5410.26441420.27562999X-RAY DIFFRACTION100
2.541-2.57880.27941430.26453101X-RAY DIFFRACTION100
2.5788-2.6190.33741370.25842975X-RAY DIFFRACTION100
2.619-2.66190.25731380.24943002X-RAY DIFFRACTION100
2.6619-2.70770.28231460.22933118X-RAY DIFFRACTION100
2.7077-2.75680.27051430.21993041X-RAY DIFFRACTION100
2.7568-2.80970.23841380.21232929X-RAY DIFFRACTION100
2.8097-2.86680.25171430.20053072X-RAY DIFFRACTION100
2.8668-2.9290.24081450.19343096X-RAY DIFFRACTION100
2.929-2.99690.24131370.18472980X-RAY DIFFRACTION100
2.9969-3.07160.25241460.17533105X-RAY DIFFRACTION100
3.0716-3.15430.21031360.16892941X-RAY DIFFRACTION100
3.1543-3.24670.21941420.16263061X-RAY DIFFRACTION100
3.2467-3.3510.20991420.15613056X-RAY DIFFRACTION100
3.351-3.47020.20941410.15392992X-RAY DIFFRACTION100
3.4702-3.60830.19231460.1463088X-RAY DIFFRACTION100
3.6083-3.77150.22051400.15312982X-RAY DIFFRACTION100
3.7715-3.96880.2181400.15493035X-RAY DIFFRACTION100
3.9688-4.21520.19821420.14553078X-RAY DIFFRACTION100
4.2152-4.53710.1581390.13523009X-RAY DIFFRACTION100
4.5371-4.9870.18971420.13963041X-RAY DIFFRACTION100
4.987-5.69350.19881430.15943060X-RAY DIFFRACTION100
5.6935-7.11730.25251400.17993006X-RAY DIFFRACTION100
7.1173-19.78570.15961430.13993033X-RAY DIFFRACTION100
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)
11.03730.00180.26471.12010.28683.6808-0.0007-0.08430.10030.12210.00420.0252-0.40040.0275-0.00410.3381-0.01660.02060.2373-0.02880.245533.254-4.5378101.3441
20.94060.0942-0.75441.3279-0.35613.4555-0.03760.0719-0.0918-0.0335-0.0322-0.01560.2264-0.01180.05540.1480.0011-0.01770.2304-0.03160.235342.9295-65.404560.6932
32.8138-0.76180.87072.7339-0.31313.85160.0087-0.08190.09510.05260.03550.3476-0.1327-0.2154-0.05230.1673-0.03210.03440.2124-0.01980.249932.8928-52.695483.9103
44.06180.7382-1.29132.8618-0.33163.36990.0410.1556-0.1018-0.1244-0.07010.2731-0.0007-0.12570.05270.35050.0016-0.02770.2611-0.02450.232132.158-16.677376.2439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 3 through 251)
2X-RAY DIFFRACTION2(chain 'A' and resid 2 through 259)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 154)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 155)

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