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- PDB-1bqs: THE CRYSTAL STRUCTURE OF MUCOSAL ADDRESSIN CELL ADHESION MOLECULE... -

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Basic information

Entry
Database: PDB / ID: 1bqs
TitleTHE CRYSTAL STRUCTURE OF MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1 (MADCAM-1)
ComponentsPROTEIN (MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1)
KeywordsMEMBRANE PROTEIN / CELL ADHESION PROTEIN / MADCAM-1 / IMMUNOGLOBULIN FOLD / I-SET FOLD / CELL ADHESION GLYCOPROTEIN / INTEGRIN RECOGINITION
Function / homology
Function and homology information


positive regulation of lymphocyte migration / integrin binding involved in cell-matrix adhesion / leukocyte tethering or rolling / positive regulation of leukocyte migration / heterotypic cell-cell adhesion / receptor clustering / Integrin cell surface interactions / cell-matrix adhesion / integrin-mediated signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...positive regulation of lymphocyte migration / integrin binding involved in cell-matrix adhesion / leukocyte tethering or rolling / positive regulation of leukocyte migration / heterotypic cell-cell adhesion / receptor clustering / Integrin cell surface interactions / cell-matrix adhesion / integrin-mediated signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell adhesion / immune response / signal transduction / membrane / plasma membrane
Similarity search - Function
Adhesion molecule, immunoglobulin-like / Mucosal addressin cell adhesion molecule 1 / Adhesion molecule, immunoglobulin-like / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins ...Adhesion molecule, immunoglobulin-like / Mucosal addressin cell adhesion molecule 1 / Adhesion molecule, immunoglobulin-like / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mucosal addressin cell adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsTan, K. / Casasnovas, J.M. / Liu, J.H. / Briskin, M.J. / Springer, T.A. / Wang, J.-H.
Citation
Journal: Structure / Year: 1998
Title: The structure of immunoglobulin superfamily domains 1 and 2 of MAdCAM-1 reveals novel features important for integrin recognition.
Authors: Tan, K. / Casasnovas, J.M. / Liu, J.H. / Briskin, M.J. / Springer, T.A. / Wang, J.H.
#1: Journal: J.Immunol. / Year: 1996
Title: Human Mucosal Addressin Cell Adhesion Molecule-1(Ma Demonstrates Structural and Functional Similarities Alpha4Beta7-Integrin Binding Domains of Murine Madc But Extreme Divergence of Mucin-Like Sequence
Authors: Shyjan, A.M. / Bertagnolli, M. / Kenney, C.J. / Briskin, M.J.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1994
Title: Traffic Signals for Lymphocyte Recirculation and Le Emigration
Authors: Springer, T.A.
History
DepositionAug 18, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 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: PROTEIN (MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3392
Polymers22,1181
Non-polymers2211
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.760, 101.100, 70.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1) / MADCAM-1


Mass: 22118.039 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR REGION WITH TWO IG-LIKE DOMAINS / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: HEMATOPOIETIC AND ENDOTHELIAL CELLS / Plasmid: PBJ5-GS-MADCAM-1 / References: UniProt: Q13477
#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.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1 (MADCAM-1) IS IMPORTANT IN LYMPHOCYTE HOMING TO MUCOSAL ...MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1 (MADCAM-1) IS IMPORTANT IN LYMPHOCYTE HOMING TO MUCOSAL TISSUES. HUMAN MADCAM-1 CONTAINS TWO IG-LIKE DOMAINS, A MUCIN-LIKE REGION, A TRANSMEMBRANE DOMAIN AND A CYTOPLASMIC DOMAIN. IT HAS A UNIQUE DUAL FUNCTION AMONG ADHESION MOLECULES. IT BINDS THE INTEGRIN ALPHA4BETA7IG-LIKE DOMAINS, AND WHEN APPROPRIATE, O-GLYCOSYLATED MOLECULES BIND THROUGH ITS MUCIN-LIKE REGION. THE FIVE C-TERMINAL RESIDUES (PTSPE) FORM THE BEGINNING OF THE MUCIN-LIKE DOMAIN.
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: 2.63 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop
Details: PROTEIN SOLUTION:17 MG/ML. CRYSTALLIZATION SOLUTION: 10% PEG 400, 0.5M LI2SO4, PH 7.5-8.0., VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Crystal grow
*PLUS
PH range low: 8 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG40001reservoir
20.5 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 1997 / Details: DOUBLE FOCUSED MIRROR
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 11229 / % possible obs: 92.2 % / Observed criterion σ(I): 3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 6.4 / % possible all: 96.1
Reflection
*PLUS
Num. measured all: 87803

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
X-PLOR3.1refinement
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→15 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.28 -10 %RANDOM
Rwork0.223 ---
obs0.223 10955 92.2 %-
Displacement parametersBiso mean: 44.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 14 79 1645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.087
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.369 -10 %
Rwork0.327 1092 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3_MOD.CHOTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.369 / % reflection Rfree: 10 % / Rfactor Rwork: 0.327

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