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- PDB-3eyq: Crystal structure of MJ5 Fab, a germline antibody variant of anti... -

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Basic information

Entry
Database: PDB / ID: 3eyq
TitleCrystal structure of MJ5 Fab, a germline antibody variant of anti-human cytomegalovirus antibody 8f9
Components
  • 8f9 Fab
  • M2J5 Fab
KeywordsIMMUNE SYSTEM / Human cytomegalovirus / antibody / Immunoglobulin domain
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / : / 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 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
Immunglobulin heavy chain variable region / IGK@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 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
C: M2J5 Fab
D: 8f9 Fab


Theoretical massNumber of molelcules
Total (without water)49,5212
Polymers49,5212
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-22.6 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.380, 76.050, 111.540
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 M2J5 Fab


Mass: 23692.338 Da / Num. of mol.: 1
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: Q6PIL8*PLUS
#2: Antibody 8f9 Fab


Mass: 25828.908 Da / Num. of mol.: 1
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: Q0ZCI9*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.6
Details: 2.6M Ammonium sulfate, 2% PEG 400, 0.1M CAPS buffer, pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 13, 2006
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 19825 / Num. obs: 19825 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.6
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 1.41 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
CNSrefinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EYF

3eyf


Resolution: 2.4→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.27 1005 Random
Rwork0.25 --
all0.25 19825 -
obs0.25 19825 -
Displacement parametersBiso mean: 23.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 0 88 3294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0227
X-RAY DIFFRACTIONc_angle_d2.18

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