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- PDB-6xnw: Crystal structure of V39A mutant of human CEACAM1 -

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Basic information

Entry
Database: PDB / ID: 6xnw
TitleCrystal structure of V39A mutant of human CEACAM1
ComponentsCarcinoembryonic antigen-related cell adhesion molecule 1
KeywordsIMMUNE SYSTEM / CEACAM1
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 epidermal growth factor receptor signaling pathway / regulation of sprouting angiogenesis / regulation of blood vessel remodeling / negative regulation of hepatocyte proliferation / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...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 epidermal growth factor receptor signaling pathway / regulation of sprouting angiogenesis / regulation of blood vessel remodeling / negative regulation of hepatocyte proliferation / 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 / filamin binding / 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 / regulation of immune system process / negative regulation of platelet aggregation / 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 / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 migration / cell-cell junction / 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 / membrane / identical protein binding / 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 / Immunoglobulin-like fold
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: 1.9 Å
AuthorsGandhi, A.K. / Kim, W.M. / Sun, Z.-Y. / Huang, Y.H. / Bonsor, D. / Petsko, G.A. / Kuchroo, V. / Blumberg, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM) United States
CitationJournal: Commun Biol / Year: 2021
Title: Structural basis of the dynamic human CEACAM1 monomer-dimer equilibrium.
Authors: Gandhi, A.K. / Sun, Z.J. / Kim, W.M. / Huang, Y.H. / Kondo, Y. / Bonsor, D.A. / Sundberg, E.J. / Wagner, G. / Kuchroo, V.K. / Petsko, G.A. / Blumberg, R.S.
History
DepositionJul 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 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_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 18, 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

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
C: Carcinoembryonic antigen-related cell adhesion molecule 1
D: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6026
Polymers47,4844
Non-polymers1172
Water27015
1
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)23,8013
Polymers23,7422
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Carcinoembryonic antigen-related cell adhesion molecule 1
D: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8013
Polymers23,7422
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.440, 91.440, 64.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-201-

NI

21C-201-

NI

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Components

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


Mass: 11871.117 Da / Num. of mol.: 4 / Mutation: V39A
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-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.005 M Cobalt(II) chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.005 M Cadmium chloride hydrate, 0.005 M Magnesium chloride hexahydrate with 12% w/v Polyethylene glycol ...Details: 0.005 M Cobalt(II) chloride hexahydrate, 0.005 M Nickel(II) chloride hexahydrate, 0.005 M Cadmium chloride hydrate, 0.005 M Magnesium chloride hexahydrate with 12% w/v Polyethylene glycol 3,350 in 0.1 M HEPES pH 7.5 buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.35
11-K, -H, -L20.155
11-h,-k,l30.256
11K, H, -L40.24
ReflectionResolution: 1.9→39.59 Å / Num. obs: 47459 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.076 / Rrim(I) all: 0.214 / Net I/σ(I): 7.8 / Num. measured all: 366913 / Scaling rejects: 134
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.947.61.6752323730480.3040.6421.7941.4100
9.11-39.597.50.06832124310.9960.0260.07318.498.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QXW

4qxw


Resolution: 1.9→39.59 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.1666 / WRfactor Rwork: 0.1306 / FOM work R set: 0.9069 / SU B: 1.237 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0194 / SU Rfree: 0.0208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.019 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 2358 5 %RANDOM
Rwork0.1449 ---
obs0.1469 45092 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.42 Å2 / Biso mean: 27.761 Å2 / Biso min: 11.16 Å2
Baniso -1Baniso -2Baniso -3
1-3.75 Å20 Å20 Å2
2--3.75 Å20 Å2
3----7.5 Å2
Refinement stepCycle: final / Resolution: 1.9→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 2 15 3373
Biso mean--21.16 26.28 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193430
X-RAY DIFFRACTIONr_bond_other_d0.0020.023168
X-RAY DIFFRACTIONr_angle_refined_deg2.2791.9414668
X-RAY DIFFRACTIONr_angle_other_deg1.24237260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3255424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.80525.682176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12315536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5771512
X-RAY DIFFRACTIONr_chiral_restr0.1410.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024032
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02828
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 172 -
Rwork0.379 3299 -
all-3471 -
obs--99.63 %

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