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- PDB-7myz: Structure of the full length 5-TM receptor CD47 bound to Fab B6H12 -

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Basic information

Entry
Database: PDB / ID: 7myz
TitleStructure of the full length 5-TM receptor CD47 bound to Fab B6H12
Components
  • B6H12 Fab heavy chain
  • B6H12 Fab light chain
  • Fusion protein of Leukocyte surface antigen CD47 an Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / 5-TM receptor / immune receptor / phagocytosis inhibitor
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 / electron transport chain / positive regulation of T cell activation / cellular response to type II interferon / positive regulation of inflammatory response / cell migration / angiogenesis / periplasmic space / electron transfer activity / iron ion binding / inflammatory response / positive regulation of cell population proliferation / apoptotic process / heme binding / 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 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Ig-like domain profile. ...Leukocyte surface antigen CD47 / CD47-like, transmembrane / CD47 immunoglobulin-like / Leukocyte surface antigen CD47, IgV / CD47 transmembrane region / CD47 immunoglobulin-like domain / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Soluble cytochrome b562 / Leukocyte surface antigen CD47
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsFenalti, G. / Villanueva, N.
CitationJournal: Nat Commun / Year: 2021
Title: Structure of the human marker of self 5-transmembrane receptor CD47.
Authors: Fenalti, G. / Villanueva, N. / Griffith, M. / Pagarigan, B. / Lakkaraju, S.K. / Huang, R.Y. / Ladygina, N. / Sharma, A. / Mikolon, D. / Abbasian, M. / Johnson, J. / Hadjivassiliou, H. / Zhu, ...Authors: Fenalti, G. / Villanueva, N. / Griffith, M. / Pagarigan, B. / Lakkaraju, S.K. / Huang, R.Y. / Ladygina, N. / Sharma, A. / Mikolon, D. / Abbasian, M. / Johnson, J. / Hadjivassiliou, H. / Zhu, D. / Chamberlain, P.P. / Cho, H. / Hariharan, K.
History
DepositionMay 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: 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.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 20, 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

Downloads & links

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Assembly

Deposited unit
C: Fusion protein of Leukocyte surface antigen CD47 an Soluble cytochrome b562
D: Fusion protein of Leukocyte surface antigen CD47 an Soluble cytochrome b562
H: B6H12 Fab heavy chain
I: B6H12 Fab heavy chain
L: B6H12 Fab light chain
M: B6H12 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,00014
Polymers186,3606
Non-polymers1,6418
Water543
1
C: Fusion protein of Leukocyte surface antigen CD47 an Soluble cytochrome b562
H: B6H12 Fab heavy chain
L: B6H12 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1578
Polymers93,1803
Non-polymers9775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-17 kcal/mol
Surface area30710 Å2
MethodPISA
2
D: Fusion protein of Leukocyte surface antigen CD47 an Soluble cytochrome b562
I: B6H12 Fab heavy chain
M: B6H12 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8436
Polymers93,1803
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-21 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.535, 53.734, 181.697
Angle α, β, γ (deg.)90.000, 92.880, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12H
22I
13L
23M

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNVALVALCA1 - 1161 - 116
21GLNGLNVALVALDB1 - 1161 - 116
12GLUGLUSERSERHC1 - 2201 - 220
22GLUGLUSERSERID1 - 2201 - 220
13ASPASPGLUGLULE1 - 2131 - 213
23ASPASPGLUGLUMF1 - 2131 - 213

NCS ensembles :
ID
1
2
3

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Components

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Antibody , 3 types, 6 molecules CDHILM

#1: Antibody Fusion protein of Leukocyte surface antigen CD47 an Soluble cytochrome b562 / Antigenic surface determinant protein OA3 / Integrin-associated protein / IAP / Protein MER6 / ...Antigenic surface determinant protein OA3 / Integrin-associated protein / IAP / Protein MER6 / Cytochrome b-562 / Antigenic surface determinant protein OA3 / Integrin-associated protein / IAP / Protein MER6


Mass: 46644.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: CD47, MER6, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08722, UniProt: P0ABE7
#2: Antibody B6H12 Fab heavy chain


Mass: 23264.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody B6H12 Fab light chain


Mass: 23270.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 1 types, 7 molecules

#4: 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.: 7
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, 4 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 100mM sodium citrate pH 6.0, 450mM ammonium acetate, 32% PEG400
PH range: 5.9-6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 35403 / % possible obs: 92.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.358 / Rpim(I) all: 0.206 / Rrim(I) all: 0.417 / Χ2: 1.389 / Net I/σ(I): 3.7 / Num. measured all: 118336
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.482.50.95919860.4560.6241.1551.04579.3
3.48-3.572.70.93220810.4960.581.1081.11982.5
3.57-3.662.80.95221910.470.5961.1341.02286.8
3.66-3.7730.85222200.4750.5121.0021.12487.8
3.77-3.893.20.68123320.5960.3990.7961.28890.8
3.89-4.033.30.65223250.6240.3820.7631.3593.4
4.03-4.193.30.53524050.7210.3090.6231.4392.8
4.19-4.383.40.45723870.790.2620.5311.32594.7
4.38-4.613.40.45824020.8160.2620.5321.83894.4
4.61-4.93.40.3624600.8590.2090.421.53295.3
4.9-5.283.50.34324310.8620.1950.3971.62395.5
5.28-5.813.80.35824650.8440.1970.4121.61496.3
5.81-6.6540.36625470.8630.1990.421.45497.7
6.65-8.373.90.25425650.930.1380.2911.32998.4
8.37-503.60.18626060.940.1060.2161.25695.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TZU

5tzu


Resolution: 3.4→48.68 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.841 / SU B: 28.196 / SU ML: 0.424 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.516 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2766 1781 5 %RANDOM
Rwork0.2527 ---
obs0.2539 33504 91.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 248.36 Å2 / Biso mean: 78.056 Å2 / Biso min: 13.28 Å2
Baniso -1Baniso -2Baniso -3
1--2.7 Å20 Å20.42 Å2
2--1.22 Å20 Å2
3---1.44 Å2
Refinement stepCycle: final / Resolution: 3.4→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9068 0 104 3 9175
Biso mean--116.01 28.13 -
Num. residues----1234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139391
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178326
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.65212839
X-RAY DIFFRACTIONr_angle_other_deg1.3431.57719266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.70851228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08522.893356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.699151359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1941530
X-RAY DIFFRACTIONr_chiral_restr0.0780.21328
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210561
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021915
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C32880.08
12D32880.08
21H62070.06
22I62070.06
31L62400.08
32M62400.08
LS refinement shellResolution: 3.4→3.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 103 -
Rwork0.282 1931 -
all-2034 -
obs--73.51 %

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