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- PDB-7sfx: 10A1 Fab in complex with CD99 peptide -

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Basic information

Entry
Database: PDB / ID: 7sfx
Title10A1 Fab in complex with CD99 peptide
Components
  • 10A1 Fab heavy chain
  • 10A1 Fab light chain
  • CD99 antigen peptide
KeywordsIMMUNE SYSTEM / tumor antigen / cytotoxic antibody / complex
Function / homology
Function and homology information


positive regulation of neutrophil extravasation / T cell extravasation / homotypic cell-cell adhesion / plasma membrane => GO:0005886 / Cell surface interactions at the vascular wall / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / focal adhesion / plasma membrane / cytoplasm
Similarity search - Function
CD99 antigen-like protein 2 / CD99 antigen like protein 2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRomero, L.A. / Hattori, T. / Koide, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2021
Title: High-valency Anti-CD99 Antibodies Toward the Treatment of T Cell Acute Lymphoblastic Leukemia.
Authors: Romero, L.A. / Hattori, T. / Ali, M.A.E. / Ketavarapu, G. / Koide, A. / Park, C.Y. / Koide, S.
History
DepositionOct 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 10A1 Fab heavy chain
D: 10A1 Fab light chain
F: CD99 antigen peptide
A: 10A1 Fab heavy chain
B: 10A1 Fab light chain
E: CD99 antigen peptide
G: 10A1 Fab heavy chain
H: 10A1 Fab light chain
J: 10A1 Fab heavy chain
K: 10A1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)201,85910
Polymers201,85910
Non-polymers00
Water18010
1
C: 10A1 Fab heavy chain
D: 10A1 Fab light chain
F: CD99 antigen peptide


  • defined by author
  • Evidence: immunoprecipitation, Yeast binding assay: Mutations to alanine on the 10A1 Fab heavy and light chain CDRs identified residues critical for CD99 binding. 10A1 and 10A1 alanine-mutants were ...Evidence: immunoprecipitation, Yeast binding assay: Mutations to alanine on the 10A1 Fab heavy and light chain CDRs identified residues critical for CD99 binding. 10A1 and 10A1 alanine-mutants were displayed on yeast in the single chain Fv format and binding towards the extracellular domain of recombinant CD99 detected., immunoprecipitation, Yeast binding assay: C-terminal truncations of the extracellular domain of CD99 containing residues 23-72 and 23-82 confirm the epitope region for clone 10A1 is similar to parental clone. 10A1 scFv was displayed on yeast and binding towards the extracellular domain of recombinant CD99 detected.
  • 51.3 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)51,2683
Polymers51,2683
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 10A1 Fab heavy chain
B: 10A1 Fab light chain
E: CD99 antigen peptide


  • defined by author
  • Evidence: immunoprecipitation, Yeast binding assay: Mutations to alanine on the 10A1 Fab heavy and light chain CDRs identified residues critical for CD99 binding. 10A1 and 10A1 alanine-mutants were ...Evidence: immunoprecipitation, Yeast binding assay: Mutations to alanine on the 10A1 Fab heavy and light chain CDRs identified residues critical for CD99 binding. 10A1 and 10A1 alanine-mutants were displayed on yeast in the single chain Fv format and binding towards the extracellular domain of recombinant CD99 detected., immunoprecipitation, Yeast binding assay: C-terminal truncations of the extracellular domain of CD99 containing residues 23-72 and 23-82 confirm the epitope region for clone 10A1 is similar to parental clone. 10A1 scFv was displayed on yeast and binding towards the extracellular domain of recombinant CD99 detected.
  • 51.3 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)51,2683
Polymers51,2683
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 10A1 Fab heavy chain
H: 10A1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,6622
Polymers49,6622
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: 10A1 Fab heavy chain
K: 10A1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)49,6622
Polymers49,6622
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.410, 131.550, 119.811
Angle α, β, γ (deg.)90.000, 90.116, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody
10A1 Fab heavy chain


Mass: 26469.451 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody
10A1 Fab light chain


Mass: 23192.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide CD99 antigen peptide / 12E7 / E2 antigen / Protein MIC2 / T-cell surface glycoprotein E2


Mass: 1605.768 Da / Num. of mol.: 2 / Fragment: sequence database residues 63-76 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P14209
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M lithium sulfate monohydrate, 0.1 M HEPES, pH 7.3, 25% PEG3350, and 0.1 M L-Proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 36430 / % possible obs: 98.9 % / Redundancy: 5.1 % / CC1/2: 0.991 / CC star: 0.998 / Rpim(I) all: 0.069 / Rrim(I) all: 0.157 / Χ2: 0.923 / Net I/σ(I): 10.97
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 4.35 / Num. unique obs: 1834 / CC1/2: 0.868 / CC star: 0.964 / Rpim(I) all: 0.198 / Rrim(I) all: 0.456 / Χ2: 0.865 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xza

2xza


Resolution: 3.1→46.38 Å / Cross valid method: FREE R-VALUE / σ(F): 187.38 / Phase error: 34.1706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2477 1882 5.22 %
Rwork0.2262 34177 -
obs0.2318 36059 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.18 Å2
Refinement stepCycle: LAST / Resolution: 3.1→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13136 0 0 10 13146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006313450
X-RAY DIFFRACTIONf_angle_d1.055218353
X-RAY DIFFRACTIONf_chiral_restr0.05312084
X-RAY DIFFRACTIONf_plane_restr0.00832353
X-RAY DIFFRACTIONf_dihedral_angle_d5.79421852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.33091440.29662392X-RAY DIFFRACTION85.37
3.18-3.280.34571390.29352633X-RAY DIFFRACTION92.71
3.28-3.380.28751270.28532652X-RAY DIFFRACTION94.21
3.38-3.50.28931390.2772649X-RAY DIFFRACTION93.54
3.5-3.640.27251390.26572604X-RAY DIFFRACTION91.56
3.64-3.810.27091360.25562642X-RAY DIFFRACTION94.39
3.81-4.010.23841680.24322661X-RAY DIFFRACTION93.47
4.01-4.260.20431110.21662678X-RAY DIFFRACTION95.34
4.26-4.590.21571750.20182643X-RAY DIFFRACTION92.83
4.59-5.050.22541280.18262652X-RAY DIFFRACTION93.05
5.05-5.780.23981150.19422684X-RAY DIFFRACTION95.38
5.78-7.280.21891500.21892661X-RAY DIFFRACTION92.72
7.28-46.380.26991760.22242661X-RAY DIFFRACTION91.89

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