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- PDB-1rih: Crystal Structure of Fab 14F7, a unique anti-tumor antibody speci... -

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Basic information

Entry
Database: PDB / ID: 1rih
TitleCrystal Structure of Fab 14F7, a unique anti-tumor antibody specific for N-glycolyl GM3
Components
  • heavy chain of antibody 14F7
  • light chain of antibody 14F7
KeywordsIMMUNE SYSTEM / Antibody / carbohydrate-binding Fab / specific for NeuGc-GM3 / immunoglobulin / beta-sheet topology
Function / homology
Function and homology information


humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / blood microparticle / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin subtype 2 / Immunoglobulin C-2 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 subtype 2 / Immunoglobulin C-2 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IgE L chain kappa / Immunoglobulin kappa constant / Ig gamma-1 chain C region secreted form / Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKrengel, U. / Olsson, L.-L. / Martinez, C. / Talavera, A. / Rojas, G. / Mier, E. / Angstrom, J. / Moreno, E.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure and Molecular Interactions of a Unique Antitumor Antibody Specific for N-Glycolyl GM3.
Authors: Krengel, U. / Olsson, L.-L. / Talavera, A. / Rojas, G. / Mier, E. / Moreno, E.
History
DepositionNov 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: diffrn_source / entity ...diffrn_source / entity / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_fragment ..._diffrn_source.pdbx_synchrotron_site / _entity.pdbx_fragment / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Aug 23, 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
L: light chain of antibody 14F7
H: heavy chain of antibody 14F7


Theoretical massNumber of molelcules
Total (without water)48,9562
Polymers48,9562
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-26 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.5, 78.9, 121.9
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody light chain of antibody 14F7


Mass: 23667.027 Da / Num. of mol.: 1 / Fragment: Fab,Fab / Source method: isolated from a natural source / Details: 14F7 mAb purified from 14F7 hybridoma cells / Source: (natural) Mus musculus (house mouse) / Cell line: 14F7 hybridoma cells / Strain: Balb/c / References: UniProt: A0A0D5ZY64, UniProt: P01837*PLUS
#2: Antibody heavy chain of antibody 14F7


Mass: 25289.395 Da / Num. of mol.: 1 / Fragment: Fab,Fab / Source method: isolated from a natural source
Details: 14F7 mAb purified from 14F7 hybridoma cells; Fab fragment prepared using papain digestion
Source: (natural) Mus musculus (house mouse) / Cell line: 14F7 hybridoma cells / Strain: Balb/c / References: UniProt: U5LP42, UniProt: P01868*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG 400, 100 mM Hepes, (25 mM Tris), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
pH: 8.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
225 mMTris1droppH8.8
315 %PEG4001reservoir
4100 mMHEPES1reservoirpH7.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22831
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMAX II I71111.093
SYNCHROTRONMAX II I71120.968
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJun 26, 2001
MARRESEARCH2CCDNov 20, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single asymmetrically cut Si (111) crystalSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0931
20.9681
ReflectionResolution: 2.5→50 Å / Num. all: 17766 / Num. obs: 17766 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 56.4 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 13.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.367 / % possible all: 97.5
Reflection shell
*PLUS
% possible obs: 97.5 %

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
AMoREphasing
CNS1.1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C5C

1c5c


Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Structure validated against composite simulated annealed OMIT maps from CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1055 -random
Rwork0.181 ---
all0.184 17766 --
obs0.184 17766 97.9 %-
Displacement parametersBiso mean: 51.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 0 37 3383
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.5-2.5400.297X-RAY DIFFRACTION798
2.54-2.580.3291310.269X-RAY DIFFRACTION834

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