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- PDB-5tz2: Crystal structure of human CD47 ECD bound to Fab of C47B222 -

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Basic information

Entry
Database: PDB / ID: 5tz2
TitleCrystal structure of human CD47 ECD bound to Fab of C47B222
Components
  • C47B222 Fab Heavy Chain
  • C47B222 Fab Light Chain
  • Leukocyte surface antigen CD47
KeywordsIMMUNE SYSTEM / antigen-Fab complex / immunoglobulin
Function / homology
Function and homology information


cellular response to interleukin-12 / regulation of Fc receptor mediated stimulatory signaling pathway / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / cell-cell adhesion mediator activity / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / regulation of type II interferon production / ATP export / fibrinogen binding ...cellular response to interleukin-12 / regulation of Fc receptor mediated stimulatory signaling pathway / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / cell-cell adhesion mediator activity / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / regulation of type II interferon production / ATP export / fibrinogen binding / regulation of tumor necrosis factor production / regulation of interleukin-12 production / regulation of nitric oxide biosynthetic process / regulation of interleukin-6 production / Signal regulatory protein family interactions / negative regulation of phagocytosis / thrombospondin receptor activity / tertiary granule membrane / cellular response to interleukin-1 / Integrin cell surface interactions / specific granule membrane / positive regulation of stress fiber assembly / positive regulation of phagocytosis / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / positive regulation of T cell activation / cellular response to type II interferon / positive regulation of inflammatory response / cell migration / angiogenesis / inflammatory response / positive regulation of cell population proliferation / apoptotic process / Neutrophil degranulation / cell surface / extracellular exosome / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...Leukocyte surface antigen CD47 / CD47-like, transmembrane / CD47 immunoglobulin-like / Leukocyte surface antigen CD47, IgV / CD47 transmembrane region / CD47 immunoglobulin-like 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
Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.302 Å
AuthorsCardoso, R.M.F.
CitationJournal: Blood Cancer J / Year: 2017
Title: Anti-leukemic activity and tolerability of anti-human CD47 monoclonal antibodies.
Authors: Pietsch, E.C. / Dong, J. / Cardoso, R. / Zhang, X. / Chin, D. / Hawkins, R. / Dinh, T. / Zhou, M. / Strake, B. / Feng, P.H. / Rocca, M. / Santos, C.D. / Shan, X. / Danet-Desnoyers, G. / Shi, ...Authors: Pietsch, E.C. / Dong, J. / Cardoso, R. / Zhang, X. / Chin, D. / Hawkins, R. / Dinh, T. / Zhou, M. / Strake, B. / Feng, P.H. / Rocca, M. / Santos, C.D. / Shan, X. / Danet-Desnoyers, G. / Shi, F. / Kaiser, E. / Millar, H.J. / Fenton, S. / Swanson, R. / Nemeth, J.A. / Attar, R.M.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: C47B222 Fab Heavy Chain
L: C47B222 Fab Light Chain
C: Leukocyte surface antigen CD47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4199
Polymers62,8143
Non-polymers1,6056
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.567, 72.934, 72.698
Angle α, β, γ (deg.)90.000, 108.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 3 types, 3 molecules HLC

#1: Antibody C47B222 Fab Heavy Chain


Mass: 24643.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody C47B222 Fab Light Chain


Mass: 23406.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Leukocyte surface antigen CD47 / Antigenic surface determinant protein OA3 / Integrin-associated protein / IAP / Protein MER6


Mass: 14764.539 Da / Num. of mol.: 1 / Fragment: extracellular domain, UNP residues 19-141 / Mutation: C15G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD47, MER6 / Cell line (production host): HEK293(GnTI-) / Production host: Homo sapiens (human) / References: UniProt: Q08722

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Sugars , 2 types, 5 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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

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Non-polymers , 2 types, 106 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.42 Å3/Da / Density % sol: 49.12 % / Mosaicity: 0.923 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3000, 1M LiCl, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→32.216 Å / Num. obs: 26271 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/av σ(I): 12.794 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.432 / CC1/2: 0.841 / % possible all: 97

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JJS

2jjs


Resolution: 2.302→32.216 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1329 5.07 %Random selection
Rwork0.2008 ---
obs0.2037 26217 98.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.2 Å2 / Biso mean: 66.5172 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.302→32.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 104 105 4197
Biso mean--100.74 66.22 -
Num. residues----539
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)
17.5857-1.4776-0.48182.188-0.56842.1393-0.0611-0.7776-0.09260.02090.02580.0980.0918-0.30050.04290.38160.1126-0.03660.5448-0.08620.351523.8982-15.493330.4121
22.8361-0.7535-0.25545.1213-1.3014.3251-0.3139-0.37370.15040.18770.2733-0.2791-0.32160.67830.09420.47990.0450.00390.6413-0.04120.367746.9462-0.16288.96
36.03570.6337-0.01983.602-3.10635.90510.00610.87040.442-0.10420.1640.11160.1001-1.0693-0.11440.46240.17-0.05790.8578-0.04070.43649.219-5.2516.3938
42.95771.4676-3.00740.4317-0.87894.2520.02430.40960.0237-0.08620.01320.0745-0.3126-0.4022-0.10910.47270.1193-0.0470.5205-0.03160.405825.5614-4.15928.2431
52.989-2.7042-1.90813.58311.57024.4928-0.11260.0628-0.23970.14390.02910.1580.4330.08780.16230.5054-0.05170.00960.41330.00550.453738.0332-7.3334-5.1594
63.6259-2.9657-1.87034.32180.54195.3783-0.07850.144-0.2229-0.3868-0.03560.11970.30390.30940.0370.5268-0.0425-0.07210.3782-0.00740.404840.6877-4.4681-6.6826
73.55640.1306-0.26234.12654.03714.94110.2519-1.5116-0.71260.5360.19460.4417-0.5599-2.04-0.12720.5718-0.1019-0.08240.82740.31720.5735-11.0017-11.427649.5232
84.5231-0.66940.87537.9232.86423.06330.4532-0.27690.0912-0.97420.03920.3260.3555-0.184-0.40070.6765-0.0228-0.00370.48270.10.5553-11.1585-16.643734.169
97.78132.14964.54815.28884.13324.4065-0.3040.8089-0.5688-0.73170.6404-0.611-1.38410.7923-0.4280.5264-0.1288-0.03040.39910.01090.39941.123-11.845239.828
108.7338-7.0848-3.84868.66583.65382.23880.62150.12060.93250.32440.8174-0.40110.75920.5161-1.26780.52850.1276-0.08380.6194-0.15310.56696.1081-20.101736.7532
118.5566-3.4322-3.37882.18320.09433.32930.2437-0.6587-0.16721.25940.996-2.06240.74391.6108-1.31640.55910.0511-0.27530.872-0.2220.8227.0435-11.677849.8986
121.83580.1266-1.14826.54815.23617.71790.2757-0.0828-0.45751.32540.2524-0.68710.90770.2625-0.46480.6378-0.0046-0.08360.48340.13550.5048-3.3791-16.323548.0279
136.5371.88232.79052.02831.9052.03090.49240.4266-0.6724-0.60830.5897-0.3044-1.0785-0.0134-0.79590.5603-0.0076-0.0040.4944-0.0070.4515-4.9516-9.155437.4278
144.49891.0298-0.06964.59435.43276.7318-0.4024-0.4020.0193-0.2462-0.05160.5842-0.6420.59590.61590.68490.0462-0.05370.49190.070.4215-8.6193-6.252845.1383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 117 )H1 - 117
2X-RAY DIFFRACTION2chain 'H' and (resid 118 through 219 )H118 - 219
3X-RAY DIFFRACTION3chain 'L' and (resid 1 through 75 )L1 - 75
4X-RAY DIFFRACTION4chain 'L' and (resid 76 through 128 )L76 - 128
5X-RAY DIFFRACTION5chain 'L' and (resid 129 through 163 )L129 - 163
6X-RAY DIFFRACTION6chain 'L' and (resid 164 through 212 )L164 - 212
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 21 )C1 - 21
8X-RAY DIFFRACTION8chain 'C' and (resid 22 through 32 )C22 - 32
9X-RAY DIFFRACTION9chain 'C' and (resid 33 through 51 )C33 - 51
10X-RAY DIFFRACTION10chain 'C' and (resid 52 through 58 )C52 - 58
11X-RAY DIFFRACTION11chain 'C' and (resid 59 through 63 )C59 - 63
12X-RAY DIFFRACTION12chain 'C' and (resid 64 through 91 )C64 - 91
13X-RAY DIFFRACTION13chain 'C' and (resid 92 through 102 )C92 - 102
14X-RAY DIFFRACTION14chain 'C' and (resid 103 through 114 )C103 - 114

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