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- PDB-7mu8: Structure of the minimally glycosylated human CEACAM1 N-terminal ... -

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Basic information

Entry
Database: PDB / ID: 7mu8
TitleStructure of the minimally glycosylated human CEACAM1 N-terminal domain
ComponentsCarcinoembryonic antigen-related cell adhesion molecule 1
KeywordsCELL ADHESION / CEACAM1 / dimer / immunoglobulin fold / glycosylated
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 / regulation of ERK1 and ERK2 cascade / basal plasma membrane / 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 / 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
Similarity search - Domain/homology
Carcinoembryonic antigen-related cell adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBelcher Dufrisne, M. / Swope, N. / Kieber, M. / Yang, J.Y. / Han, J. / Li, J. / Moremen, K.W. / Prestegard, J.H. / Columbus, L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM087828 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM131829 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103390 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM136076 United States
CitationJournal: Structure / Year: 2022
Title: Human CEACAM1 N-domain dimerization is independent from glycan modifications.
Authors: Belcher Dufrisne, M. / Swope, N. / Kieber, M. / Yang, J.Y. / Han, J. / Li, J. / Moremen, K.W. / Prestegard, J.H. / Columbus, L.
History
DepositionMay 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)25,47916
Polymers23,7982
Non-polymers1,68114
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, assay for oligomerization, Nitroxide labeled cysteine mutants of the CEACAM1 N-terminal domain were assessed using continuous wave (CW) and double electron-electron ...Evidence: gel filtration, assay for oligomerization, Nitroxide labeled cysteine mutants of the CEACAM1 N-terminal domain were assessed using continuous wave (CW) and double electron-electron resonance (DEER) electron paramagnetic resonance (EPR) spectroscopy, supporting the dimer conformation in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-1 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.455, 93.455, 134.665
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 2 or resid 4...
21(chain B and (resid 1 through 2 or resid 4...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLEULEU(chain A and (resid 1 through 2 or resid 4...AA1 - 21 - 2
12THRTHRGLYGLY(chain A and (resid 1 through 2 or resid 4...AA4 - 144 - 14
13GLNGLNTYRTYR(chain A and (resid 1 through 2 or resid 4...AA1 - 1071 - 107
14GLNGLNTYRTYR(chain A and (resid 1 through 2 or resid 4...AA1 - 1071 - 107
15GLNGLNTYRTYR(chain A and (resid 1 through 2 or resid 4...AA1 - 1071 - 107
16GLNGLNTYRTYR(chain A and (resid 1 through 2 or resid 4...AA1 - 1071 - 107
17GLNGLNTYRTYR(chain A and (resid 1 through 2 or resid 4...AA1 - 1071 - 107
18GLNGLNTYRTYR(chain A and (resid 1 through 2 or resid 4...AA1 - 1071 - 107
21GLNGLNLEULEU(chain B and (resid 1 through 2 or resid 4...BB1 - 21 - 2
22THRTHRTHRTHR(chain B and (resid 1 through 2 or resid 4...BB4 - 524 - 52
23GLNGLNGLNGLN(chain B and (resid 1 through 2 or resid 4...BB5353
24GLNGLNTYRTYR(chain B and (resid 1 through 2 or resid 4...BB1 - 1071 - 107
25GLNGLNTYRTYR(chain B and (resid 1 through 2 or resid 4...BB1 - 1071 - 107
26GLNGLNTYRTYR(chain B and (resid 1 through 2 or resid 4...BB1 - 1071 - 107
27GLNGLNTYRTYR(chain B and (resid 1 through 2 or resid 4...BB1 - 1071 - 107

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Components

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


Mass: 11899.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM1, BGP, BGP1 / Plasmid: pGen2 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P13688
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM MES, pH 6.5, 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→46.73 Å / Num. obs: 25094 / % possible obs: 99.8 % / Redundancy: 11.2 % / Biso Wilson estimate: 27.35 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07249 / Rpim(I) all: 0.02249 / Rrim(I) all: 0.07597 / Net I/σ(I): 12.88
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 11.5 % / Rmerge(I) obs: 2.009 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 3588 / CC1/2: 0.494 / CC star: 0.813 / Rpim(I) all: 0.6181 / Rrim(I) all: 2.103 / % possible all: 99.89

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QXW

4qxw


Resolution: 1.7→46.7 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 1290 5.15 %
Rwork0.2022 23781 -
obs0.2025 25070 99.76 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.11 Å2 / Biso mean: 33.79 Å2 / Biso min: 18.33 Å2
Refinement stepCycle: final / Resolution: 1.7→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 107 98 1869
Biso mean--53.16 36.82 -
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081815
X-RAY DIFFRACTIONf_angle_d1.0232467
X-RAY DIFFRACTIONf_dihedral_angle_d22.919649
X-RAY DIFFRACTIONf_chiral_restr0.063279
X-RAY DIFFRACTIONf_plane_restr0.006317
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A953X-RAY DIFFRACTION12.71TORSIONAL
12B953X-RAY DIFFRACTION12.71TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.76810.28271430.25422605100
1.7681-1.84860.24811320.24612646100
1.8486-1.9460.26371330.23872625100
1.946-2.06790.25941400.2218258999
2.0679-2.22760.23171560.22732631100
2.2276-2.45180.22731180.22132663100
2.4518-2.80650.24621410.22572656100
2.8065-3.53570.23791530.2022658100
3.5357-44.90380.17611740.1693270899

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