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- PDB-5yax: Crystal structure of a human neutralizing antibody bound to a HBV... -

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Basic information

Entry
Database: PDB / ID: 5yax
TitleCrystal structure of a human neutralizing antibody bound to a HBV preS1 peptide
Components
  • Large envelope protein
  • scFv1 antibody
KeywordsIMMUNE SYSTEM / HBV / NTCP / preS1 / antibody / Fc receptor
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Large envelope protein S / Major surface antigen from hepadnavirus / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Large envelope protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLiu, X. / Zheng, S. / Ye, K. / Sui, J.
CitationJournal: Elife / Year: 2017
Title: A potent human neutralizing antibody Fc-dependently reduces established HBV infections
Authors: Li, D. / He, W. / Liu, X. / Zheng, S. / Qi, Y. / Li, H. / Mao, F. / Liu, J. / Sun, Y. / Pan, L. / Du, K. / Ye, K. / Li, W. / Sui, J.
History
DepositionSep 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: scFv1 antibody
B: scFv1 antibody
C: Large envelope protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0184
Polymers57,9953
Non-polymers231
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-16 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.670, 55.662, 67.696
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-101-

NA

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Components

#1: Antibody scFv1 antibody


Mass: 25737.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: scFv / Production host: Escherichia coli (E. coli)
#2: Protein Large envelope protein


Mass: 6520.975 Da / Num. of mol.: 1 / Fragment: PreS1 peptide, UNP residues 2-59
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Strain: isolate S472-20 / Production host: Escherichia coli (E. coli) / References: UniProt: B2CXZ0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 19392 / % possible obs: 96 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.144 / Χ2: 1.656 / Net I/σ(I): 17.7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 886 / Χ2: 1.114 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.5→19.923 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2879 937 5.13 %
Rwork0.2424 --
obs0.2448 18261 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→19.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3513 0 1 227 3741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023596
X-RAY DIFFRACTIONf_angle_d0.5724893
X-RAY DIFFRACTIONf_dihedral_angle_d12.3511272
X-RAY DIFFRACTIONf_chiral_restr0.023537
X-RAY DIFFRACTIONf_plane_restr0.003631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.63150.35241450.29452502X-RAY DIFFRACTION99
2.6315-2.7960.49351250.37392391X-RAY DIFFRACTION93
2.796-3.01120.29481380.26872567X-RAY DIFFRACTION100
3.0112-3.3130.29371450.24992589X-RAY DIFFRACTION100
3.313-3.78950.28771140.24612188X-RAY DIFFRACTION84
3.7895-4.76360.21421470.17312301X-RAY DIFFRACTION88
4.7636-19.9240.20591230.18422786X-RAY DIFFRACTION100

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