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- PDB-3v6z: Crystal Structure of Hepatitis B Virus e-antigen -

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Basic information

Entry
Database: PDB / ID: 3v6z
TitleCrystal Structure of Hepatitis B Virus e-antigen
Components
  • Fab e6 Heavy Chain
  • Fab e6 Light Chain
  • e-antigen
KeywordsIMMUNE SYSTEM / dimer inversion / four-helix bundle
Function / homology
Function and homology information


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 / Immunoglobulins / Immunoglobulin-like / Sandwich ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHepatitis B virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsDimattia, M.A. / Watts, N.R. / Stahl, S.J. / Grimes, J.M. / Steven, A.C. / Stuart, D.I. / Wingfield, P.T.
CitationJournal: Structure / Year: 2013
Title: Antigenic switching of hepatitis B virus by alternative dimerization of the capsid protein.
Authors: Dimattia, M.A. / Watts, N.R. / Stahl, S.J. / Grimes, J.M. / Steven, A.C. / Stuart, D.I. / Wingfield, P.T.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab e6 Heavy Chain
B: Fab e6 Light Chain
C: Fab e6 Heavy Chain
D: Fab e6 Light Chain
E: e-antigen
F: e-antigen


Theoretical massNumber of molelcules
Total (without water)131,9506
Polymers131,9506
Non-polymers00
Water0
1
A: Fab e6 Heavy Chain
B: Fab e6 Light Chain
F: e-antigen


Theoretical massNumber of molelcules
Total (without water)65,9753
Polymers65,9753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-31 kcal/mol
Surface area27150 Å2
MethodPISA
2
C: Fab e6 Heavy Chain
D: Fab e6 Light Chain
E: e-antigen


Theoretical massNumber of molelcules
Total (without water)65,9753
Polymers65,9753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-31 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.660, 75.760, 88.700
Angle α, β, γ (deg.)96.77, 103.81, 116.04
Int Tables number1
Space group name H-MP1
DetailsHepatitis B virus e-antigen (HBeAg) is comprised of chains E and F / antibody Fab e6 fragment is comprised of two chains, one light (chains B or D) and one heavy (chains A or C). / one HBeAg-Fab complex involves one HBeAg and two Fabs, or the chains A-F of the crystal ASU.

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Components

#1: Antibody Fab e6 Heavy Chain


Mass: 23765.408 Da / Num. of mol.: 2 / Fragment: Fab e6 Heavy Chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab e6 Light Chain


Mass: 24329.928 Da / Num. of mol.: 2 / Fragment: Fab e6 Light Chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein e-antigen


Mass: 17879.451 Da / Num. of mol.: 2 / Fragment: HBV e-antigen (Cp(-10)149) / Mutation: C48A, C107A, G123A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Gene: preC/C / References: UniProt: Q9QMH8

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.05 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.34→46.2 Å / Num. obs: 19664 / % possible obs: 92.6 % / Biso Wilson estimate: 76.24 Å2

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.34→46.2 Å / Cor.coef. Fo:Fc: 0.8793 / Cor.coef. Fo:Fc free: 0.8901 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE ROBS, RWORK AND RFREE VALUES ARE VERY CLOSE DUE TO THE USE OF TARGET RESTRAINTS DURING REFINEMENT FOR THE FAB MOLECULES TO A PREVIOUSLY-DETERMINED HIGHER RESOLUTION STRUCTURE (2.3 ...Details: THE ROBS, RWORK AND RFREE VALUES ARE VERY CLOSE DUE TO THE USE OF TARGET RESTRAINTS DURING REFINEMENT FOR THE FAB MOLECULES TO A PREVIOUSLY-DETERMINED HIGHER RESOLUTION STRUCTURE (2.3 ANGSTROM; PDB ID 3V6F) (SMART ET AL., 2012)
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 1004 5.11 %RANDOM
Rwork0.234 ---
obs0.234 19651 92.62 %-
Displacement parametersBiso mean: 110.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.5488 Å2-8.6258 Å2-8.9658 Å2
2---6.3674 Å216.7917 Å2
3---4.8185 Å2
Refine analyzeLuzzati coordinate error obs: 0.937 Å
Refinement stepCycle: LAST / Resolution: 3.34→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9082 0 0 0 9082
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089302HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1912699HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3005SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes174HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1353HARMONIC5
X-RAY DIFFRACTIONt_it9302HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion21.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1242SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10209SEMIHARMONIC4
LS refinement shellResolution: 3.34→3.52 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2781 134 4.84 %
Rwork0.246 2635 -
all0.2475 2769 -
obs--92.62 %
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)
18.11630.23081.67473.60320.59475.15770.1487-0.2225-0.37280.2763-0.44630.32450.1821-0.13360.2976-0.0565-0.0196-0.0746-0.41740.00790.2337-5.8528-8.054965.6961
25.51-1.26860.82394.9691-3.00231.93240.2379-0.19620.1505-0.312-0.03630.1347-0.6114-0.0333-0.20150.30810.14310.0554-0.244-0.0194-0.191415.647217.093160.6451
38.1033-1.9239-1.75674.23181.38857.79080.23080.02840.1363-0.1734-0.49520.1667-0.0535-0.04730.2644-0.08840.0125-0.0575-0.36380.06830.0152-6.1585-36.3018.6852
47.4969-0.87691.4545.4521-2.38132.61220.14490.104-0.28050.0939-0.0978-0.05190.437-0.4641-0.04710.27530.1045-0.0684-0.26090.0811-0.213115.4538-61.362913.7987
55.2731.8776-2.36563.49470.25045.6164-0.18770.6372-0.2001-0.1502-0.29230.18560.2812-0.10980.48-0.21020.2259-0.1301-0.0697-0.1240.0782-3.5084-10.396644.5177
66.45480.18992.50555.21610.90648.93390.2509-0.0798-0.1085-0.0338-0.3233-0.1464-0.28380.35690.0724-0.0135-0.0450.0961-0.27360.1858-0.120527.352112.397650.9139
73.81720.93012.18943.39990.00128.9825-0.007-0.74820.30270.1362-0.15720.24420.08030.30020.1642-0.2776-0.13570.0594-0.0981-0.04610.0433-3.5894-33.659729.8124
89.5569-1.1865-2.91223.3454-0.11026.89170.1254-0.0251-0.037-0.0534-0.1389-0.22370.09220.5010.0135-0.0170.2462-0.0063-0.15530.192-0.119627.1767-56.617223.3532
95.5111-4.1621-2.36482.95970.81742.48540.1889-0.09980.22910.03820.0059-0.0014-0.1869-0.4332-0.1948-0.410.12250.0318-0.0926-0.16090.2674-35.6645-23.01920.0986
104.44144.41441.32694.08341.60381.18590.08720.0963-0.14980.04960.0168-0.15290.1282-0.5412-0.104-0.42330.03130.0096-0.0582-0.16580.2732-35.5085-21.184954.3545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 123}A1 - 123
2X-RAY DIFFRACTION2{A|124 - 224}A124 - 224
3X-RAY DIFFRACTION3{C|1 - 123}C1 - 123
4X-RAY DIFFRACTION4{C|124 - 224}C124 - 224
5X-RAY DIFFRACTION5{B|1 - 115}B1 - 115
6X-RAY DIFFRACTION6{B|116 - 219}B116 - 219
7X-RAY DIFFRACTION7{D|1 - 115}D1 - 115
8X-RAY DIFFRACTION8{D|116 - 219}D116 - 219
9X-RAY DIFFRACTION9{E|4 - 151}E4 - 151
10X-RAY DIFFRACTION10{F|4 - 151}F4 - 151

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