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- PDB-4qxw: Crystal structure of the human CEACAM1 membrane distal amino term... -

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Basic information

Entry
Database: PDB / ID: 4qxw
TitleCrystal structure of the human CEACAM1 membrane distal amino terminal (N)-domain
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 / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of sprouting angiogenesis / regulation of blood vessel remodeling / regulation of epidermal growth factor receptor signaling pathway / negative regulation of hepatocyte proliferation / filamin binding ...regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of sprouting angiogenesis / regulation of blood vessel remodeling / regulation of epidermal growth factor receptor signaling pathway / negative regulation of hepatocyte proliferation / filamin binding / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of lipid biosynthetic process / bile acid transmembrane transporter activity / 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 / positive regulation of vasculogenesis / cell-cell adhesion via plasma-membrane adhesion molecules / negative regulation of platelet aggregation / regulation of immune system process / bile acid and bile salt transport / negative regulation of vascular permeability / wound healing, spreading of cells / transport vesicle membrane / microvillus membrane / negative regulation of T cell receptor signaling pathway / blood vessel development / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / lateral plasma membrane / specific granule membrane / regulation of cell migration / basal plasma membrane / regulation of ERK1 and ERK2 cascade / protein tyrosine kinase binding / 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 ...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
MALONIC ACID / Carcinoembryonic antigen-related cell adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsHuang, Y.H. / Gandhi, A.K. / Russell, A. / 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
DepositionJul 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Non-polymer description
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4875
Polymers23,7982
Non-polymers6893
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-3 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.160, 107.160, 61.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

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


Mass: 11899.170 Da / Num. of mol.: 2 / Fragment: N terminal domain
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
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM TrisHCL buffer 7.5, 60% Tascimate 8.0, 1% Beta-octyl glucoside, 12% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 23, 2012
RadiationMonochromator: channel-cut Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.04→47.923 Å / Num. all: 23421 / Num. obs: 23379 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 22.94 Å2 / Rmerge(I) obs: 0.198 / Net I/σ(I): 8.8 / Scaling rejects: 154
Reflection shellResolution: 2.04→2.1 Å / Redundancy: 9 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 2.3 / Num. measured all: 16250 / Num. unique all: 1802 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
Aimless0.1.26data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
CBASSdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→47.923 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 21.68 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 1202 5.14 %RANDOM
Rwork0.2039 ---
all0.2059 23421 --
obs0.2059 23379 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.88 Å2 / Biso mean: 23.9286 Å2 / Biso min: 12.58 Å2
Refinement stepCycle: LAST / Resolution: 2.04→47.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 47 66 1793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081762
X-RAY DIFFRACTIONf_angle_d1.0972395
X-RAY DIFFRACTIONf_chiral_restr0.042260
X-RAY DIFFRACTIONf_plane_restr0.005312
X-RAY DIFFRACTIONf_dihedral_angle_d20.994684
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.04-2.12170.26041220.246724422564100
2.1217-2.21830.31821440.228123852529100
2.2183-2.33520.2641290.228224392568100
2.3352-2.48150.2661440.225124142558100
2.4815-2.67310.29771360.238224362572100
2.6731-2.94210.26611330.23124552588100
2.9421-3.36770.24651210.207324882609100
3.3677-4.24260.24121220.173625122634100
4.2426-47.93660.17641510.17142606275799

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