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- PDB-1gsm: A reassessment of the MAdCAM-1 structure and its role in integrin... -

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Basic information

Entry
Database: PDB / ID: 1gsm
TitleA reassessment of the MAdCAM-1 structure and its role in integrin recognition.
ComponentsMUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1
KeywordsCELL ADHESION PROTEIN / MADCAM-1 / IMMUNOGLOBULIN FOLD / I-SET FOLD / CELL ADHESION GLYCOPROTEIN / INTEGRIN RECOGINITION / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of lymphocyte migration / integrin binding involved in cell-matrix adhesion / leukocyte tethering or rolling / heterotypic cell-cell adhesion / positive regulation of leukocyte migration / 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 / heterotypic cell-cell adhesion / positive regulation of leukocyte migration / 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 / Immunoglobulins / Immunoglobulin-like fold ...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 / Immunoglobulins / Immunoglobulin-like fold / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDando, J. / Wilkinson, K.W. / Ortlepp, S. / King, D.J. / Brady, R.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: A Reassessment of the Madcam-1 Structure and its Role in Integrin Recognition
Authors: Dando, J. / Wilkinson, K.W. / Ortlepp, S. / King, D.J. / Brady, R.L.
History
DepositionJan 8, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1


Theoretical massNumber of molelcules
Total (without water)22,2941
Polymers22,2941
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.000, 99.200, 70.500
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 MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1 / MADCAM-1


Mass: 22294.299 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR REGION WITH TWO IG-LIKE DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: HEMATOPOIETIC AND ENDOTHELIAL CELLS / Cell line (production host): NSO CELLS / Production host: MUS MUSCULUS (house mouse) / References: UniProt: Q13477
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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.
Sequence detailsTHE CONSTRUCT WAS DESIGNED WITH A C-TERMINAL XA CLEAVAGE SITE THE C-TERMINAL FOUR RESIDUES ARE PART ...THE CONSTRUCT WAS DESIGNED WITH A C-TERMINAL XA CLEAVAGE SITE THE C-TERMINAL FOUR RESIDUES ARE PART OF THIS CONSTRUCT

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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: 2.51 Å3/Da / Density % sol: 43.3 %
Crystal growpH: 8
Details: PROTEIN SOLUTION:10 MG/ML. CRYSTALLIZATION SOLUTION: 16% PEG 4000, 0.5M LI2SO4, PH 7.75.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris1droppH8.0
316 %(w/v)PEG40001reservoir
40.5 M1reservoirLi2SO4
50.1 MTris1reservoirpH7.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 102574 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 43.3
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 99 %
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BQS

1bqs


Resolution: 1.9→29.49 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.747 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ATOMS WHICH WERE NOT VISIBLE IN THE ELECTRON DENSITY MAPS HAVE BEEN GIVEN ZERO OCCUPANCY IN THIS PDB FILE.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 901 5.1 %RANDOM
Rwork0.217 ---
obs0.218 16764 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.9→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 0 184 1715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211452
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.8581.9821988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021106
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.3563
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.5228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.354
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3070.536
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0631.5970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93521559
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8853482
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7634.5429
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 54
Rwork0.224 1185
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.223 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.2166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d0.032
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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