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- PDB-2gk2: Crystal structure of the N terminal domain of human CEACAM1 -

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Basic information

Entry
Database: PDB / ID: 2gk2
TitleCrystal structure of the N terminal domain of human CEACAM1
ComponentsCarcinoembryonic antigen-related cell adhesion molecule 1
KeywordsCELL ADHESION / immunoglobulin domain / adhesion protein
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
NICKEL (II) ION / Carcinoembryonic antigen-related cell adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFedarovich, A. / Tomberg, J. / Nicholas, R.A. / Davies, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of the N-terminal domain of human CEACAM1: binding target of the opacity proteins during invasion of Neisseria meningitidis and N. gonorrhoeae.
Authors: Fedarovich, A. / Tomberg, J. / Nicholas, R.A. / Davies, C.
History
DepositionMar 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)24,7377
Polymers24,3432
Non-polymers3945
Water1,35175
1
A: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4144
Polymers12,1711
Non-polymers2433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3223
Polymers12,1711
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules

A: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules

A: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules

B: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules

B: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules

B: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,21021
Polymers73,0296
Non-polymers1,18115
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation4_654-x+1,-y,z-1/21
crystal symmetry operation5_554y,-x+y,z-1/21
crystal symmetry operation6_544x-y,x-1,z-1/21
Buried area9820 Å2
ΔGint-56 kcal/mol
Surface area27000 Å2
MethodPISA
4
A: Carcinoembryonic antigen-related cell adhesion molecule 1
B: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules

A: Carcinoembryonic antigen-related cell adhesion molecule 1
B: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules

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)74,21021
Polymers73,0296
Non-polymers1,18115
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area8150 Å2
ΔGint-58 kcal/mol
Surface area28660 Å2
MethodPISA
5
A: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules

B: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7377
Polymers24,3432
Non-polymers3945
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554y,-x+y,z-1/21
Buried area2060 Å2
ΔGint-10 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.2, 86.2, 62.0
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-200-

NI

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Components

#1: Protein Carcinoembryonic antigen-related cell adhesion molecule 1 / Biliary glycoprotein 1 / BGP-1 / CD66 antigen / CD66a antigen


Mass: 12171.431 Da / Num. of mol.: 2 / Fragment: N terminal domain (residues 63-170)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM1 / Plasmid: pGEX-2V / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P13688
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#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.: 75 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% (w/v) polyethylene glycol mono methyl ether 2000, 100 mM Tris, and 5 mM nickel chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 13366 / Num. obs: 13366 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 38.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2 / Num. unique all: 1290 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L6Z

1l6z


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.806 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.258 657 4.9 %RANDOM
Rwork0.21 ---
all0.213 13361 --
obs0.213 13361 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 20 75 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221765
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9492399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2875218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.65125.7389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62315273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.258156
X-RAY DIFFRACTIONr_chiral_restr0.1050.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021370
X-RAY DIFFRACTIONr_nbd_refined0.2360.21108
X-RAY DIFFRACTIONr_nbtor_refined0.3240.21227
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2171
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.215
X-RAY DIFFRACTIONr_mcbond_it0.4741.51098
X-RAY DIFFRACTIONr_mcangle_it0.86221753
X-RAY DIFFRACTIONr_scbond_it1.4933738
X-RAY DIFFRACTIONr_scangle_it2.44.5646
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.53 54 -
Rwork0.404 901 -
obs-955 96.37 %
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)
13.1387-0.18681.60462.126-0.3123.3745-0.0883-0.17460.15120.02480.00170.2593-0.0049-0.1780.0866-0.1638-0.00260.0019-0.1683-0.0836-0.141429.9373-14.5867-1.2784
24.0122-0.9284-0.88364.15082.55334.55790.05170.1898-0.2899-0.1717-0.06090.02590.04060.12310.0091-0.08830.0133-0.0307-0.1112-0.1263-0.061632.49474.372710.1942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 1073 - 111
2X-RAY DIFFRACTION2BB-3 - 1071 - 111

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