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- PDB-6xo1: Crystal structure of N97A mutant of human CEACAM1 -

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Basic information

Entry
Database: PDB / ID: 6xo1
TitleCrystal structure of N97A 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: 1.758 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 5, 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)23,9204
Polymers23,7122
Non-polymers2082
Water3,261181
1
A: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9602
Polymers11,8561
Non-polymers1041
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)11,9602
Polymers11,8561
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.934, 56.879, 124.541
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 11856.145 Da / Num. of mol.: 2 / Mutation: N97A
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.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 6% Tascimate with 25% polyethylene glycol 400 in 0.1 M MES monohydrate pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.758→28.76 Å / Num. obs: 19429 / % possible obs: 96.1 % / Redundancy: 11.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 19.5
Reflection shellResolution: 1.758→1.8 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1087 / CC1/2: 0.794

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Processing

Software
NameVersionClassification
REFMAC5.8.0135 2015/10/01refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QXW

4qxw


Resolution: 1.758→28.76 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.815 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 980 -RANDOM
Rwork0.1918 18418 --
all0.194 ---
obs-19398 96.111 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.631 Å2
Baniso -1Baniso -2Baniso -3
1-0.521 Å20 Å2-0 Å2
2--0.28 Å20 Å2
3----0.801 Å2
Refinement stepCycle: LAST / Resolution: 1.758→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 14 181 1871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191724
X-RAY DIFFRACTIONr_bond_other_d0.0020.021594
X-RAY DIFFRACTIONr_angle_refined_deg1.9161.9492346
X-RAY DIFFRACTIONr_angle_other_deg1.04433654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1195212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.42425.58186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19515268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.183156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022020
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02410
X-RAY DIFFRACTIONr_nbd_refined0.2560.2834
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.23022
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21698
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21882
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.294
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2510.265
X-RAY DIFFRACTIONr_nbd_other0.2380.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.27
X-RAY DIFFRACTIONr_mcbond_it1.1221.324854
X-RAY DIFFRACTIONr_mcbond_other1.1211.324853
X-RAY DIFFRACTIONr_mcangle_it1.5421.981064
X-RAY DIFFRACTIONr_mcangle_other1.5421.981065
X-RAY DIFFRACTIONr_scbond_it2.5041.658869
X-RAY DIFFRACTIONr_scbond_other2.4841.653867
X-RAY DIFFRACTIONr_scangle_it3.8042.3731282
X-RAY DIFFRACTIONr_scangle_other3.8042.3731282
X-RAY DIFFRACTIONr_lrange_it5.11411.9351953
X-RAY DIFFRACTIONr_lrange_other5.07711.9321952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.758-1.8030.716640.7021019148373.02760.702
1.803-1.8530.577630.4731115140084.14290.473
1.853-1.9060.386590.2961194140489.2450.296
1.906-1.9650.31480.1881287133999.70130.188
1.965-2.0290.209740.171123313071000.171
2.029-2.10.23730.189123113041000.189
2.1-2.1780.264620.179113311951000.179
2.178-2.2670.265580.179112911871000.179
2.267-2.3670.209510.176110011511000.176
2.367-2.4820.217690.174101610851000.174
2.482-2.6150.186500.17198610361000.171
2.615-2.7720.206500.1719239731000.171
2.772-2.9610.236520.1758919431000.175
2.961-3.1960.216520.1768138651000.176
3.196-3.4960.222330.1697748071000.169
3.496-3.9020.195330.1557077401000.155
3.902-4.4920.183320.1486216531000.148
4.492-5.4680.176250.1795375621000.179
5.468-7.5970.32190.2344344531000.234
7.597-28.7620.196130.2022752881000.202

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