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- PDB-6xno: Crystal structure of E99A mutant of human CEACAM1 -

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Basic information

Entry
Database: PDB / ID: 6xno
TitleCrystal structure of E99A 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 / 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 / Immunoglobulin-like fold
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: 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 3, 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

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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)24,4756
Polymers23,6822
Non-polymers7934
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-11 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.820, 106.820, 62.230
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: 11841.134 Da / Num. of mol.: 2 / Mutation: E99A
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.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 3.75 Å3/Da / Density % sol: 67.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 41% Tascimate with 0.5 % n-Octyl-D-glucoside pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→75.53 Å / Num. obs: 28973 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.034 / Rrim(I) all: 0.127 / Net I/σ(I): 14.3 / Num. measured all: 393727 / Scaling rejects: 159
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
1.9-1.9413.31.4522452218430.7690.4071.5092.3100
9.11-75.5310.50.04534043230.9780.0160.04832.899

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QXW

4qxw


Resolution: 1.9→75.53 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.929 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 1403 4.8 %RANDOM
Rwork0.1894 ---
obs0.191 27541 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: 88.91 Å2 / Biso mean: 31.081 Å2 / Biso min: 16.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å2-0 Å2-0 Å2
2--1.09 Å2-0 Å2
3----2.17 Å2
Refinement stepCycle: final / Resolution: 1.9→75.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 54 86 1814
Biso mean--55.84 38.15 -
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191762
X-RAY DIFFRACTIONr_bond_other_d0.0020.021642
X-RAY DIFFRACTIONr_angle_refined_deg2.1521.9682394
X-RAY DIFFRACTIONr_angle_other_deg1.02933772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0025212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.51525.58186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11515266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.226156
X-RAY DIFFRACTIONr_chiral_restr0.1310.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022024
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02414
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 115 -
Rwork0.276 1968 -
all-2083 -
obs--99.86 %

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