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- PDB-1l6z: CRYSTAL STRUCTURE OF MURINE CEACAM1A[1,4]: A CORONAVIRUS RECEPTOR... -

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Basic information

Entry
Database: PDB / ID: 1l6z
TitleCRYSTAL STRUCTURE OF MURINE CEACAM1A[1,4]: A CORONAVIRUS RECEPTOR AND CELL ADHESION MOLECULE IN THE CEA FAMILY
Componentsbiliary glycoprotein C
KeywordsCELL ADHESION / Ig-like domain / CEA Family / Coronavirus Receptor
Function / homology
Function and homology information


Fibronectin matrix formation / granulocyte colony-stimulating factor receptor binding / positive regulation of homophilic cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / 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 ...Fibronectin matrix formation / granulocyte colony-stimulating factor receptor binding / positive regulation of homophilic cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / 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 epidermal growth factor receptor signaling pathway / negative regulation of hepatocyte proliferation / regulation of blood vessel remodeling / 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 / insulin catabolic process / Cell surface interactions at the vascular wall / common myeloid progenitor cell proliferation / Toll-like receptor binding / 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 / cell-cell junction organization / negative regulation of vascular permeability / negative regulation of bone resorption / wound healing, spreading of cells / bile acid and bile salt transport / negative regulation of cytokine production / ciliary membrane / microvillus membrane / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of T cell receptor signaling pathway / blood vessel development / negative regulation of osteoclast differentiation / lateral plasma membrane / negative regulation of T cell proliferation / transport vesicle / Neutrophil degranulation / regulation of ERK1 and ERK2 cascade / basal plasma membrane / protein tyrosine kinase binding / regulation of cell growth / adherens junction / negative regulation of protein kinase activity / cellular response to insulin stimulus / cell-cell junction / cell junction / virus receptor activity / calmodulin binding / protein dimerization activity / cell adhesion / apical plasma membrane / external side of plasma membrane / protein kinase binding / cell surface / signal transduction / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / 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 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
: / Carcinoembryonic antigen-related cell adhesion molecule 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, Molecular Replacement / Resolution: 3.32 Å
AuthorsTan, K. / Zelus, B.D. / Meijers, R. / Liu, J.-H. / Bergelson, J.M. / Duke, N. / Zhang, R. / Joachimiak, A. / Holmes, K.V. / Wang, J.-H.
CitationJournal: Embo J. / Year: 2002
Title: CRYSTAL STRUCTURE OF MURINE sCEACAM1a[1,4]: A CORONAVIRUS RECEPTOR IN THE CEA FAMILY
Authors: Tan, K. / Zelus, B.D. / Meijers, R. / Liu, J.-H. / Bergelson, J.M. / Duke, N. / Zhang, R. / Joachimiak, A. / Holmes, K.V. / Wang, J.-H.
History
DepositionMar 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: biliary glycoprotein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7845
Polymers24,5341
Non-polymers1,2504
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.26, 111.26, 65.64
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein biliary glycoprotein C / biliary glycoprotein C / CD66a


Mass: 24533.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Murine CEACAM1A / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec.3.2.8.1 / References: PIR: JC1507, UniProt: P31809*PLUS
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.78 Å3/Da / Density % sol: 74.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 10% PEG 8000, 0.2 M magnesium acetate, 0.1 M cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMTris1droppH7.6
2150 mM1dropNaCl
35 %glycerol1drop
40.5-1 mgprotein1drop
510 %PEG80001reservoir
60.2 Mmagnesium acetate1reservoir
70.1 Mcacodylate1reservoirpH6.4

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.0715,1.0718,1.0534
SYNCHROTRONAPS 19-ID21.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 6, 2001
ADSC QUANTUM 42CCDFeb 6, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GraphiteMADMx-ray1
2GraphiteMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.07151
21.07181
31.05341
41.11
ReflectionResolution: 3.32→30 Å / Num. all: 7127 / Num. obs: 6979 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 68.14 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.3
Reflection shellResolution: 3.32→3.42 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.7 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 7127 / % possible obs: 99.7 % / Num. measured all: 123640
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
MLPHAREphasing
AMoREphasing
X-PLOR3.851refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD, Molecular Replacement
Starting model: PDB ENTRIES 1HNF AND 1E4J

1hnf

1e4j


Resolution: 3.32→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.329 754 Random
Rwork0.295 --
all0.297 6898 -
obs0.297 6898 -
Refine analyze
FreeObs
Luzzati coordinate error0.672 Å0.581 Å
Luzzati d res low-5 Å
Luzzati sigma a1.124 Å0.998 Å
Refinement stepCycle: LAST / Resolution: 3.32→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 81 26 1716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg2.325
LS refinement shellResolution: 3.32→3.45 Å /
RfactorNum. reflection
Rfree0.577 70
Rwork0.456 -
obs-676
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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