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- PDB-4whd: Human CEACAM1 N-domain homodimer -

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Basic information

Entry
Database: PDB / ID: 4whd
TitleHuman CEACAM1 N-domain homodimer
ComponentsCarcinoembryonic antigen-related cell adhesion molecule 1
KeywordsPROTEIN BINDING / dimer / CEACAM
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 / negative regulation of hepatocyte proliferation / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / filamin binding ...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 / negative regulation of hepatocyte proliferation / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / filamin binding / regulation of blood vessel remodeling / 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 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / insulin catabolic process / Fibronectin matrix formation / common myeloid progenitor cell proliferation / cell-cell adhesion via plasma-membrane adhesion molecules / negative regulation of interleukin-1 production / negative regulation of fatty acid biosynthetic process / positive regulation of vasculogenesis / negative regulation of platelet aggregation / bile acid transmembrane transporter activity / negative regulation of vascular permeability / regulation of immune system process / wound healing, spreading of cells / negative regulation of T cell receptor signaling pathway / microvillus membrane / bile acid and bile salt transport / transport vesicle membrane / blood vessel development / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / lateral plasma membrane / regulation of ERK1 and ERK2 cascade / specific granule membrane / regulation of cell migration / protein tyrosine kinase binding / basal plasma membrane / negative regulation of protein kinase activity / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / adherens junction / regulation of cell growth / kinase binding / cellular response to insulin stimulus / cell junction / cell-cell junction / cell migration / actin binding / protein phosphatase binding / angiogenesis / calmodulin binding / protein dimerization activity / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell adhesion molecule CEACAM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsKirouac, K.N. / Prive, G.G.
CitationJournal: To Be Published
Title: Human CEACAM1 N-domain homodimer
Authors: Kirouac, K.N. / Prive, G.G.
History
DepositionSep 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Dec 27, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)26,55613
Polymers23,9402
Non-polymers2,61511
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint25 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.573, 107.573, 63.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 0 - 107 / Label seq-ID: 1 - 108

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 11970.249 Da / Num. of mol.: 2 / Fragment: N-domain (UNP residues 34-141)
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: 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.: 8 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.86 Å3/Da / Density % sol: 68.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: PEG 3000, NaCl, Phosphate-Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→76.07 Å / Num. obs: 13472 / % possible obs: 99 % / Redundancy: 1.8 % / Net I/σ(I): 18.63

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.5→76.07 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / SU B: 13.593 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 1264 9.9 %RANDOM
Rwork0.1828 ---
obs0.1872 11450 94.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 119.83 Å2 / Biso mean: 18.888 Å2 / Biso min: 5.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.94 Å2
Refinement stepCycle: final / Resolution: 2.5→76.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1691 0 147 137 1975
Biso mean--69.33 26.72 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021886
X-RAY DIFFRACTIONr_bond_other_d0.0040.021810
X-RAY DIFFRACTIONr_angle_refined_deg1.6472.012544
X-RAY DIFFRACTIONr_angle_other_deg1.44934176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.42725.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12815274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.743157
X-RAY DIFFRACTIONr_chiral_restr0.2090.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212066
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02425
X-RAY DIFFRACTIONr_mcbond_it1.4321.198869
X-RAY DIFFRACTIONr_mcbond_other1.4221.197868
X-RAY DIFFRACTIONr_mcangle_it2.1951.7891085
Refine LS restraints NCS

Ens-ID: 1 / Number: 6167 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 79 -
Rwork0.235 777 -
all-856 -
obs--87.98 %
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)
10.82660.51230.43063.24931.68833.40860.00810.04920.0414-0.0674-0.06650.099-0.14140.07380.05840.0503-0.04860.01250.07-0.01270.016614.367-38.87620.431
22.89881.0421-1.61421.3823-0.90063.2072-0.0633-0.1489-0.08350.01390.0175-0.0737-0.09390.2830.04590.0748-0.0396-0.00260.0631-0.00330.006811.274-36.32246.176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 107
2X-RAY DIFFRACTION2B0 - 107

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