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- PDB-2jjs: Structure of human CD47 in complex with human signal regulatory p... -

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Basic information

Entry
Database: PDB / ID: 2jjs
TitleStructure of human CD47 in complex with human signal regulatory protein (SIRP) alpha
Components
  • LEUKOCYTE SURFACE ANTIGEN CD47
  • TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
KeywordsCELL ADHESION / SIGNAL REGULATORY PROTEIN ALPHA / IMMUNOGLOBULIN SUPERFAMILY / TRANSMEMBRANE / PHOSPHOPROTEIN / PAIRED RECEPTOR / POLYMORPHISM / GLYCOPROTEIN / PYRROLIDONE CARBOXYLIC ACID / ALTERNATIVE SPLICING / IMMUNOGLOBULIN DOMAIN / SIRP / CD47 / SIRPA / MEMBRANE / SH3-BINDING
Function / homology
Function and homology information


negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / regulation of interleukin-1 beta production / regulation of type II interferon production ...negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / regulation of interleukin-1 beta production / regulation of type II interferon production / cell-cell adhesion mediator activity / ATP export / GTPase regulator activity / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / protein antigen binding / negative regulation of nitric oxide biosynthetic process / negative regulation of interferon-beta production / negative regulation of JNK cascade / regulation of tumor necrosis factor production / regulation of interleukin-12 production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / regulation of interleukin-6 production / Signal regulatory protein family interactions / thrombospondin receptor activity / tertiary granule membrane / negative regulation of interleukin-6 production / ficolin-1-rich granule membrane / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / cellular response to interleukin-1 / Integrin cell surface interactions / specific granule membrane / positive regulation of phagocytosis / positive regulation of stress fiber assembly / protein tyrosine kinase binding / negative regulation of protein phosphorylation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / negative regulation of ERK1 and ERK2 cascade / cellular response to hydrogen peroxide / negative regulation of inflammatory response / SH3 domain binding / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of T cell activation / cell migration / regulation of gene expression / protein phosphatase binding / angiogenesis / cellular response to lipopolysaccharide / cell adhesion / inflammatory response / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Leukocyte surface antigen CD47 / CD47-like, transmembrane / CD47 immunoglobulin-like / Leukocyte surface antigen CD47, IgV / CD47 transmembrane region / CD47 immunoglobulin-like domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...Leukocyte surface antigen CD47 / CD47-like, transmembrane / CD47 immunoglobulin-like / Leukocyte surface antigen CD47, IgV / CD47 transmembrane region / CD47 immunoglobulin-like domain / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Tyrosine-protein phosphatase non-receptor type substrate 1 / Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHatherley, D. / Graham, S.C. / Turner, J. / Harlos, K. / Stuart, D.I. / Barclay, A.N.
CitationJournal: Mol. Cell / Year: 2008
Title: Paired receptor specificity explained by structures of signal regulatory proteins alone and complexed with CD47.
Authors: Hatherley, D. / Graham, S.C. / Turner, J. / Harlos, K. / Stuart, D.I. / Barclay, A.N.
History
DepositionApr 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other / Structure summary
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct / struct_biol / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct.title / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 2.0Mar 11, 2020Group: Data collection / Other / Polymer sequence / Category: chem_comp / entity_poly / pdbx_database_status
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
B: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
C: LEUKOCYTE SURFACE ANTIGEN CD47
D: LEUKOCYTE SURFACE ANTIGEN CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,48728
Polymers56,8764
Non-polymers3,61224
Water9,728540
1
A: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
C: LEUKOCYTE SURFACE ANTIGEN CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,24414
Polymers28,4382
Non-polymers1,80612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-5.9 kcal/mol
Surface area14300 Å2
MethodPQS
2
B: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
D: LEUKOCYTE SURFACE ANTIGEN CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,24414
Polymers28,4382
Non-polymers1,80612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-6.1 kcal/mol
Surface area14820 Å2
MethodPQS
Unit cell
Length a, b, c (Å)42.477, 72.410, 89.826
Angle α, β, γ (deg.)90.00, 95.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1 / SIRP ALPHA / SHP SUBSTRATE 1 / SHPS-1 / INHIBITORY RECEPTOR SHPS-1 / SIGNAL REGULATORY PROTEIN ...SIRP ALPHA / SHP SUBSTRATE 1 / SHPS-1 / INHIBITORY RECEPTOR SHPS-1 / SIGNAL REGULATORY PROTEIN ALPHA-1 / SIRP-ALPHA-1 / SIRP-ALPHA-2 / SIRP-ALPHA- 3 / MYD-1 ANTIGEN / BRAIN IG-LIKE MOLECULE WITH TYROSINE- BASED ACTIVATION MOTIFS / BIT / MACROPHAGE FUSION RECEPTOR / P84 / CD172A ANTIGEN


Mass: 13919.563 Da / Num. of mol.: 2 / Fragment: N-TERMINAL ECTODOMAIN, RESIDUES 31-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEE14 / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: P78324
#2: Antibody LEUKOCYTE SURFACE ANTIGEN CD47 / CD47 / INTEGRIN-ASSOCIATED PROTEIN / IAP / ANTIGENIC SURFACE DETERMINANT PROTEIN OA3 / PROTEIN MER6


Mass: 14518.302 Da / Num. of mol.: 2
Fragment: IMMUNOGLOBULIN-SUPERFAMILY ECTODOMAIN, RESIDUES 19-136
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEE14 / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: Q08722
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN C, CYS 33 TO GLY ENGINEERED RESIDUE IN CHAIN D, CYS 33 TO GLY
Sequence detailsSIRP ALPHA (CHAINS A AND B) RESIDUE NUMBERING IS FOR THE MATURE PROTEIN (LACKING N-TERMINAL 30 ...SIRP ALPHA (CHAINS A AND B) RESIDUE NUMBERING IS FOR THE MATURE PROTEIN (LACKING N-TERMINAL 30 AMINO ACID SIGNAL SEQUENCE). C-TERMINAL PURIFICATION TAG (TRHHHHHH) IS ADDED. CD47 RESIDUE NUMBERING IS FOR MATURE PROTEIN (LACKING N- TERMINAL 18 AMINO ACID SIGNAL SEQUENCE). RESIDUE 1 (GLN) CYCLISES TO FORM A PYROGLUTAMIC ACID. RESIDUE 15 WAS MUTATED FROM CYS TO GLY. C-TERMINAL PURIFICATION TAG ( STRHHHHHH) IS ADDED.

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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: 2.4 Å3/Da / Density % sol: 49.3 % / Description: NONE
Crystal growTemperature: 278 K / pH: 7.4
Details: 100 NL SIRP ALPHA / CD47 COMPLEX (1:1 RATIO, EACH PROTEIN AT APPROX. 0.375 UM) PLUS 100 NL RESERVOIR (0.2 M POTASSIUM IODIDE, 20% W/V PEG 3350) EQUILIBRATED AGAINST 95 UL OF RESERVOIR AT 5 C., pH 7.4

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID23-210.873
SYNCHROTRONESRF BM1421.5498
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDApr 15, 2007MIRRORS
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111) MONOCHROMATORSINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.8731
21.54981
ReflectionResolution: 1.85→29.8 Å / Num. obs: 46373 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.6
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UV3 FOR CHAINS A AND B, PDB ENTRY 2ICC FOR CHAINS C AND D

2uv3

2icc


Resolution: 1.85→89.44 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.986 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B VALUES INCLUDE TLS CONTRIBUTIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2345 5.1 %RANDOM
Rwork0.169 ---
obs0.171 43948 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0.09 Å2
2--0.34 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.85→89.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 102 540 4268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223797
X-RAY DIFFRACTIONr_bond_other_d0.0010.022563
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9865158
X-RAY DIFFRACTIONr_angle_other_deg0.8423.0036243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17624.615156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.86715644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2911518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02726
X-RAY DIFFRACTIONr_nbd_refined0.1870.2452
X-RAY DIFFRACTIONr_nbd_other0.1940.22455
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21731
X-RAY DIFFRACTIONr_nbtor_other0.0980.21940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2366
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.70822345
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4733795
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.96141566
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.38161361
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 168
Rwork0.221 3208
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.134-0.1592-0.18861.0986-0.06761.2427-0.03890.01220.0020.02530.01270.02140.0138-0.13840.0262-0.0958-0.0330.0142-0.0566-0.0075-0.163916.63-7.4940.631
20.78770.15470.0181.2321-0.06310.8614-0.01480.054-0.0208-0.04050.00040.02050.0236-0.01960.0144-0.1249-0.0023-0.0043-0.08750.0077-0.166519.4240.2383.744
30.40950.1615-0.0170.61670.2882.41530.03730.001-0.03160.0563-0.0486-0.01150.12770.04250.0113-0.1007-0.0284-0.0062-0.09680.0009-0.147231.37-21.16321.74
40.6687-0.3992-0.16810.85090.41352.0707-0.051-0.09470.05810.03740.0883-0.0225-0.12190.0458-0.0373-0.11610.00020.0028-0.08660.0094-0.14531.04714.73425.197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 116
2X-RAY DIFFRACTION2B1 - 119
3X-RAY DIFFRACTION3C1 - 116
4X-RAY DIFFRACTION4D1 - 116

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