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- PDB-5dzl: Crystal structure of the protein human CEACAM1 -

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Basic information

Entry
Database: PDB / ID: 5dzl
TitleCrystal structure of the protein human CEACAM1
ComponentsCarcinoembryonic antigen-related cell adhesion molecule 1
KeywordsCELL ADHESION
Function / homology
Function and homology information


regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / Regulation of MITF-M dependent genes involved in invasion / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / negative regulation of hepatocyte proliferation / regulation of blood vessel remodeling ...regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / Regulation of MITF-M dependent genes involved in invasion / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / negative regulation of hepatocyte proliferation / regulation of blood vessel remodeling / filamin binding / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of lipid biosynthetic process / negative regulation of T cell mediated cytotoxicity / regulation of endothelial cell migration / negative regulation of granulocyte differentiation / Fibronectin matrix formation / insulin catabolic process / common myeloid progenitor cell proliferation / negative regulation of interleukin-1 production / negative regulation of fatty acid biosynthetic process / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of vasculogenesis / bile acid transmembrane transporter activity / regulation of immune system process / negative regulation of platelet aggregation / negative regulation of vascular permeability / wound healing, spreading of cells / bile acid and bile salt transport / microvillus membrane / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of T cell receptor signaling pathway / transport vesicle membrane / blood vessel development / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / lateral plasma membrane / specific granule membrane / regulation of cell migration / protein tyrosine kinase binding / regulation of ERK1 and ERK2 cascade / basal plasma membrane / integrin-mediated signaling pathway / regulation of cell growth / Cell surface interactions at the vascular wall / adherens junction / negative regulation of protein kinase activity / kinase binding / cellular response to insulin stimulus / cell-cell junction / cell migration / cell junction / actin binding / protein phosphatase binding / angiogenesis / protein dimerization activity / calmodulin binding / cell adhesion / apical plasma membrane / Neutrophil degranulation / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Carcinoembryonic antigen-related cell adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4006 Å
AuthorsHuang, Y.H. / Russell, A. / Gandhi, A.K. / Kondo, Y. / Chen, Q. / Petsko, G.A. / Blumberg, R.S.
CitationJournal: Nature / Year: 2015
Title: CEACAM1 regulates TIM-3-mediated tolerance and exhaustion.
Authors: Huang, Y.H. / Zhu, C. / Kondo, Y. / Anderson, A.C. / Gandhi, A. / Russell, A. / Dougan, S.K. / Petersen, B.S. / Melum, E. / Pertel, T. / Clayton, K.L. / Raab, M. / Chen, Q. / Beauchemin, N. ...Authors: Huang, Y.H. / Zhu, C. / Kondo, Y. / Anderson, A.C. / Gandhi, A. / Russell, A. / Dougan, S.K. / Petersen, B.S. / Melum, E. / Pertel, T. / Clayton, K.L. / Raab, M. / Chen, Q. / Beauchemin, N. / Yazaki, P.J. / Pyzik, M. / Ostrowski, M.A. / Glickman, J.N. / Rudd, C.E. / Ploegh, H.L. / Franke, A. / Petsko, G.A. / Kuchroo, V.K. / Blumberg, R.S.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionOct 7, 2015ID: 4QYC
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Structure summary
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carcinoembryonic antigen-related cell adhesion molecule 1
B: Carcinoembryonic antigen-related cell adhesion molecule 1
C: Carcinoembryonic antigen-related cell adhesion molecule 1
D: Carcinoembryonic antigen-related cell adhesion molecule 1


Theoretical massNumber of molelcules
Total (without water)47,9454
Polymers47,9454
Non-polymers00
Water00
1
A: Carcinoembryonic antigen-related cell adhesion molecule 1
B: Carcinoembryonic antigen-related cell adhesion molecule 1


Theoretical massNumber of molelcules
Total (without water)23,9722
Polymers23,9722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-8 kcal/mol
Surface area10140 Å2
MethodPISA
2
C: Carcinoembryonic antigen-related cell adhesion molecule 1
D: Carcinoembryonic antigen-related cell adhesion molecule 1


Theoretical massNumber of molelcules
Total (without water)23,9722
Polymers23,9722
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-9 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.760, 75.760, 147.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Carcinoembryonic antigen-related cell adhesion molecule 1 / Biliary glycoprotein 1 / BGP-1


Mass: 11986.249 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM1, BGP, BGP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13688

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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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris 8.0, 25% PEG 3350, 12% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2014
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→36.88 Å / Num. obs: 6397 / % possible obs: 99.9 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.245 / Net I/σ(I): 6.5
Reflection shellResolution: 3.4→3.72 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 6.5 / Num. measured obs: 1474 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QXW

4qxw


Resolution: 3.4006→36.855 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2877 291 4.63 %
Rwork0.2321 5998 -
obs0.2346 6289 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.79 Å2 / Biso mean: 33.3492 Å2 / Biso min: 14.71 Å2
Refinement stepCycle: final / Resolution: 3.4006→36.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 0 0 3366
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053438
X-RAY DIFFRACTIONf_angle_d0.9084684
X-RAY DIFFRACTIONf_chiral_restr0.034521
X-RAY DIFFRACTIONf_plane_restr0.004621
X-RAY DIFFRACTIONf_dihedral_angle_d15.1331238
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4006-4.28330.31471440.2762877302198
4.2833-36.85710.26371470.19731213268100

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