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- PDB-6nmt: Non-Blocking Fab 3 anti-SIRP-alpha antibody in complex with SIRP-... -

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Basic information

Entry
Database: PDB / ID: 6nmt
TitleNon-Blocking Fab 3 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1
Components
  • Fab 3 anti-SIRP-alpha antibody Variable Heavy Chain
  • Fab 3 anti-SIRP-alpha antibody Variable Light Chain
  • Tyrosine-protein phosphatase non-receptor type substrate 1
KeywordsIMMUNE SYSTEM / SIRP-alpha / Signal regulatory protein alpha / Signal-regulatory protein alpha / Tyrosine-protein phosphatase non-receptor type substrate 1 / CD47 / Cluster of Differentiation 47 / anti-SIRP-alpha antibody / Blocking anti-SIRP-alpha antibody / Non-Blocking anti-SIRP-alpha antibody / Kick-Off anti-SIRP-alpha antibody / anti-SIRP-alpha antibody in complex with SIRP-alpha
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 / cell-cell adhesion mediator activity / regulation of type II interferon production / negative regulation of nitric oxide biosynthetic process ...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 / cell-cell adhesion mediator activity / regulation of type II interferon production / negative regulation of nitric oxide biosynthetic process / protein antigen binding / negative regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of interferon-beta production / regulation of tumor necrosis factor production / negative regulation of JNK cascade / regulation of nitric oxide biosynthetic process / regulation of interleukin-6 production / Signal regulatory protein family interactions / negative regulation of phagocytosis / protein phosphatase inhibitor activity / negative regulation of interleukin-6 production / tertiary granule membrane / ficolin-1-rich granule membrane / negative regulation of tumor necrosis factor production / cellular response to interleukin-1 / positive regulation of phagocytosis / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / protein tyrosine kinase binding / Cell surface interactions at the vascular wall / negative regulation of ERK1 and ERK2 cascade / SH3 domain binding / cellular response to type II interferon / positive regulation of T cell activation / negative regulation of inflammatory response / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / 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 / Resolution: 1.83 Å
AuthorsWibowo, A.S. / Carter, J.J. / Sim, J.
CitationJournal: Mabs / Year: 2019
Title: Discovery of high affinity, pan-allelic, and pan-mammalian reactive antibodies against the myeloid checkpoint receptor SIRP alpha.
Authors: Sim, J. / Sockolosky, J.T. / Sangalang, E. / Izquierdo, S. / Pedersen, D. / Harriman, W. / Wibowo, A.S. / Carter, J. / Madan, A. / Doyle, L. / Harrabi, O. / Kauder, S.E. / Chen, A. / Kuo, T. ...Authors: Sim, J. / Sockolosky, J.T. / Sangalang, E. / Izquierdo, S. / Pedersen, D. / Harriman, W. / Wibowo, A.S. / Carter, J. / Madan, A. / Doyle, L. / Harrabi, O. / Kauder, S.E. / Chen, A. / Kuo, T.C. / Wan, H. / Pons, J.
History
DepositionJan 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab 3 anti-SIRP-alpha antibody Variable Light Chain
B: Fab 3 anti-SIRP-alpha antibody Variable Heavy Chain
C: Tyrosine-protein phosphatase non-receptor type substrate 1


Theoretical massNumber of molelcules
Total (without water)60,3303
Polymers60,3303
Non-polymers00
Water11,800655
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance, Binding kinetics of Fab 119 anti-SIRP-alpha antibody with SIRP-alpha in competition with CD47.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.370, 126.370, 229.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11C-304-

HOH

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Components

#1: Antibody Fab 3 anti-SIRP-alpha antibody Variable Light Chain


Mass: 22416.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab 3 anti-SIRP-alpha antibody Variable Heavy Chain


Mass: 23881.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: 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: 14031.807 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: Homo sapiens (human) / References: UniProt: P78324
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / 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: 3.8 Å3/Da / Density % sol: 67.63 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium Acetate, 0.45 M Ammonium Sulfate, 35% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2017
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.83→63.19 Å / Num. obs: 81726 / % possible obs: 100 % / Redundancy: 12.8 % / Rsym value: 0.105 / Net I/σ(I): 15.2
Reflection shellResolution: 1.83→1.85 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5960 / Rsym value: 0.031 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.83→63.19 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.643 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.094
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 4189 5.1 %RANDOM
Rwork0.1776 ---
obs0.1789 77537 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.4 Å2 / Biso mean: 39.295 Å2 / Biso min: 21.94 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.83→63.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4019 0 0 655 4674
Biso mean---49.67 -
Num. residues----537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194149
X-RAY DIFFRACTIONr_bond_other_d0.0020.023765
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9555648
X-RAY DIFFRACTIONr_angle_other_deg1.0338770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7755545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49923.929168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37515662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2461526
X-RAY DIFFRACTIONr_chiral_restr0.1290.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214681
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02837
LS refinement shellResolution: 1.83→1.878 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 322 -
Rwork0.322 5635 -
all-5957 -
obs--99.95 %

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