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- PDB-7kpg: Blocking Fab 25 anti-SIRP-alpha antibody in complex with SIRP-alp... -

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Basic information

Entry
Database: PDB / ID: 7kpg
TitleBlocking Fab 25 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1
Components
  • Heavy chain of Fab 25 anti-SIRP-alpha antibody
  • Light chain of Fab 25 anti-SIRP-alpha antibody
  • Tyrosine-protein phosphatase non-receptor type substrate 1
KeywordsSIGNALING PROTEIN / SIRPa antibody complex / signal regulatory protein alpha variant 1
Function / homology
Function and homology information


cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / protein binding involved in heterotypic cell-cell adhesion / negative regulation of chemokine (C-C motif) ligand 5 production / regulation of interleukin-1 beta production / GTPase regulator activity / regulation of type II interferon production / cell-cell adhesion mediator activity / negative regulation of lipopolysaccharide-mediated signaling pathway ...cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / protein binding involved in heterotypic cell-cell adhesion / negative regulation of chemokine (C-C motif) ligand 5 production / regulation of interleukin-1 beta production / GTPase regulator activity / regulation of type II interferon production / cell-cell adhesion mediator activity / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of nitric oxide biosynthetic process / negative regulation of interferon-beta production / regulation of tumor necrosis factor production / protein antigen binding / regulation of interleukin-6 production / regulation of nitric oxide biosynthetic process / negative regulation of JNK cascade / Signal regulatory protein family interactions / protein phosphatase inhibitor activity / negative regulation of interleukin-6 production / negative regulation of phagocytosis / tertiary granule membrane / negative regulation of tumor necrosis factor production / ficolin-1-rich granule membrane / cellular response to interleukin-1 / negative regulation of cytokine production involved in inflammatory response / positive regulation of phagocytosis / protein tyrosine kinase binding / negative regulation of canonical NF-kappaB signal transduction / Cell surface interactions at the vascular wall / cellular response to type II interferon / negative regulation of ERK1 and ERK2 cascade / negative regulation of inflammatory response / SH3 domain binding / positive regulation of reactive oxygen species metabolic process / cellular response to hydrogen peroxide / positive regulation of T cell activation / cell migration / regulation of gene expression / protein phosphatase binding / cell adhesion / Neutrophil degranulation / cell surface / extracellular exosome / membrane / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
Tyrosine-protein phosphatase non-receptor type substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsSim, J. / Pons, J.
CitationJournal: J Hematol Oncol / Year: 2020
Title: Targeting the myeloid checkpoint receptor SIRP alpha potentiates innate and adaptive immune responses to promote anti-tumor activity.
Authors: Kuo, T.C. / Chen, A. / Harrabi, O. / Sockolosky, J.T. / Zhang, A. / Sangalang, E. / Doyle, L.V. / Kauder, S.E. / Fontaine, D. / Bollini, S. / Han, B. / Fu, Y.X. / Sim, J. / Pons, J. / Wan, H.I.
History
DepositionNov 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Heavy chain of Fab 25 anti-SIRP-alpha antibody
L: Light chain of Fab 25 anti-SIRP-alpha antibody
S: Tyrosine-protein phosphatase non-receptor type substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1988
Polymers57,7173
Non-polymers4805
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Running SEC after complexation to show shift in retention volume for larger complex formation.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-94 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.160, 189.160, 78.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody Heavy chain of Fab 25 anti-SIRP-alpha antibody


Mass: 22566.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Antibody Light chain of Fab 25 anti-SIRP-alpha antibody


Mass: 22648.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Tyrosine-protein phosphatase non-receptor type substrate 1 / SHPS-1 / Brain Ig-like molecule with tyrosine-based activation motifs / Bit / CD172 antigen-like ...SHPS-1 / Brain Ig-like molecule with tyrosine-based activation motifs / Bit / CD172 antigen-like family member A / Inhibitory receptor SHPS-1 / Macrophage fusion receptor / MyD-1 antigen / Signal-regulatory protein alpha-1 / Sirp-alpha-1 / Signal-regulatory protein alpha-2 / Sirp-alpha-2 / Signal-regulatory protein alpha-3 / Sirp-alpha-3 / p84


Mass: 12502.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRPA, BIT, MFR, MYD1, PTPNS1, SHPS1, SIRP / Production host: Escherichia coli (E. coli) / References: UniProt: P78324
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 28% w/v PEG 8000, 0.1 M citric acid pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Mar 26, 2019
RadiationMonochromator: Micromax Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.27→61.92 Å / Num. obs: 38395 / % possible obs: 99.6 % / Redundancy: 13.5 % / CC1/2: 1 / Rsym value: 0.176 / Net I/σ(I): 10.9
Reflection shellResolution: 2.27→2.32 Å / Num. unique obs: 2803 / CC1/2: 1 / Rsym value: 1.73

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UV3

2uv3


Resolution: 2.27→61.92 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.495 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2819 1972 5.1 %RANDOM
Rwork0.2342 ---
obs0.2367 36422 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.15 Å2 / Biso mean: 39.689 Å2 / Biso min: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 2.27→61.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 25 166 4231
Biso mean--74.31 36.28 -
Num. residues----539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0144170
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173618
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.6685691
X-RAY DIFFRACTIONr_angle_other_deg0.8471.6378504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3525537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62922.67176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28215631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3751518
X-RAY DIFFRACTIONr_chiral_restr0.0680.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024678
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02766
LS refinement shellResolution: 2.27→2.329 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 166 -
Rwork0.327 2635 -
all-2801 -
obs--99.93 %

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