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- PDB-3eyf: Crystal structure of anti-human cytomegalovirus antibody 8f9 plus... -

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Basic information

Entry
Database: PDB / ID: 3eyf
TitleCrystal structure of anti-human cytomegalovirus antibody 8f9 plus gB peptide
Components
  • 8f9 Fab
  • AD-2
  • Synthetic peptide
KeywordsIMMUNE SYSTEM / cytomegalovirus / antibody / Immunoglobulin domain / Cleavage on pair of basic residues / Envelope protein / Glycoprotein / Host-virus interaction / Membrane / Transmembrane / Virion
Function / homology
Function and homology information


immunoglobulin complex / host cell Golgi membrane / host cell endosome membrane / adaptive immune response / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular region ...immunoglobulin complex / host cell Golgi membrane / host cell endosome membrane / adaptive immune response / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular region / membrane / plasma membrane
Similarity search - Function
Herpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / : / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain ...Herpesvirus Glycoprotein B, antigenic domain, N-terminal / Glycoprotein B N-terminal antigenic domain of HCMV / : / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein B / Ig-like domain-containing protein / IGK@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsThomson, C.A. / Bryson, S. / McLean, G.R. / Creagh, A.L. / Pai, E.F. / Schrader, J.W.
CitationJournal: Embo J. / Year: 2008
Title: Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus.
Authors: Thomson, C.A. / Bryson, S. / McLean, G.R. / Creagh, A.L. / Pai, E.F. / Schrader, J.W.
History
DepositionOct 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 5, 2017Group: Database references / Category: struct_ref / struct_ref_seq
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 8f9 Fab
B: AD-2
C: 8f9 Fab
D: AD-2
E: Synthetic peptide
F: Synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9668
Polymers101,7826
Non-polymers1842
Water7,242402
1
A: 8f9 Fab
B: AD-2
E: Synthetic peptide


Theoretical massNumber of molelcules
Total (without water)50,8913
Polymers50,8913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-32.6 kcal/mol
Surface area19640 Å2
MethodPISA
2
C: 8f9 Fab
D: AD-2
F: Synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0755
Polymers50,8913
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-31 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.300, 103.500, 152.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 8f9 Fab


Mass: 23714.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6PJF2*PLUS
#2: Antibody AD-2


Mass: 25932.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET40 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q68CN4*PLUS
#3: Protein/peptide Synthetic peptide


Mass: 1244.394 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic peptide following the sequence of residues 69-78 of Glycoprotein B from Human cytomegalovirus, UniProt entry P13201 (VGLB_HCMVT)
References: UniProt: P13201
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.6
Details: 1.9M Ammonium sulfate, 0.1M CAPS buffer, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2005
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 42862 / Num. obs: 42862 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 4.5 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HEZ

1hez


Resolution: 2.3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.23 2137 Random
Rwork0.21 --
all0.21 42862 -
obs0.21 42862 -
Displacement parametersBiso mean: 36.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6699 0 12 402 7113
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0206
X-RAY DIFFRACTIONc_angle_deg2.26

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