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- PDB-4hd9: Crystal structure of native human MAdCAM-1 D1D2 domain -

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Basic information

Entry
Database: PDB / ID: 4hd9
TitleCrystal structure of native human MAdCAM-1 D1D2 domain
ComponentsMucosal addressin cell adhesion molecule 1
KeywordsIMMUNE SYSTEM / immunoglobulin superfamily / rolling and firm adhesion / integrin alpha4beta7
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: 1.7 Å
AuthorsSpringer, T. / Yu, Y. / Zhu, J.
CitationJournal: TO BE PUBLISHED
Title: A Different Fold with an Integrin-Binding Loop Specialized for Flexibility in Mucosal Addressin Cell Adhesion Molecule-1
Authors: Springer, T. / Yu, Y. / Zhu, J. / Wang, J.-H. / Huang, P.-S.
History
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: Mucosal addressin cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5702
Polymers22,3481
Non-polymers2211
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.476, 99.988, 69.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-599-

HOH

21A-602-

HOH

31A-623-

HOH

41A-645-

HOH

51A-646-

HOH

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Components

#1: Protein Mucosal addressin cell adhesion molecule 1 / MAdCAM-1 / hMAdCAM-1


Mass: 22348.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MADCAM1 / Organ (production host): OVARY / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec3.2.8.1 / 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.: 247 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG4K, 0.5M Li2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2003
RadiationMonochromator: Cryogenically-cooled double crystal Si(111) monochromator.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→22.56 Å / Num. all: 23698 / Num. obs: 23698 / % possible obs: 72.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→22.56 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 2232 9.81 %Random
Rwork0.1711 ---
all0.177 22754 --
obs0.1753 22754 90.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→22.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 14 247 1727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091692
X-RAY DIFFRACTIONf_angle_d1.3412335
X-RAY DIFFRACTIONf_dihedral_angle_d14.35648
X-RAY DIFFRACTIONf_chiral_restr0.072277
X-RAY DIFFRACTIONf_plane_restr0.007315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73710.2885510.2357490X-RAY DIFFRACTION36
1.7371-1.77750.3667850.2568787X-RAY DIFFRACTION57
1.7775-1.82190.23841110.23781134X-RAY DIFFRACTION80
1.8219-1.87120.26411640.22371300X-RAY DIFFRACTION93
1.8712-1.92620.2151180.19741353X-RAY DIFFRACTION96
1.9262-1.98830.20481630.17821393X-RAY DIFFRACTION99
1.9883-2.05930.22731480.17711382X-RAY DIFFRACTION99
2.0593-2.14170.20181530.15881382X-RAY DIFFRACTION100
2.1417-2.23910.18721720.15671379X-RAY DIFFRACTION99
2.2391-2.35710.20291420.16251428X-RAY DIFFRACTION100
2.3571-2.50460.23441620.17271389X-RAY DIFFRACTION99
2.5046-2.69760.22531600.17091416X-RAY DIFFRACTION99
2.6976-2.96860.22691510.15941410X-RAY DIFFRACTION99
2.9686-3.39690.22071440.16321413X-RAY DIFFRACTION98
3.3969-4.27490.19441430.15441425X-RAY DIFFRACTION98
4.2749-22.56150.20371650.17831441X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.5499-1.94174.21192.3823-1.81146.1738-0.07840.48240.2820.0725-0.1205-0.3967-0.38961.0310.16810.1473-0.0523-0.01730.23620.03880.153448.75464.972731.5211
25.4713-0.86530.69077.3440.45755.7867-0.0233-0.1102-0.15910.3286-0.04350.02810.11130.43140.06380.1361-0.0042-0.01440.17750.02380.113753.341954.31837.8851
35.7936-0.36935.05662.7987-0.20086.49590.23350.0358-0.3225-0.14080.02670.05140.25590.2016-0.25510.1688-0.0458-0.01930.11490.03110.136147.905158.465637.1132
45.1885-0.84462.43050.3203-0.80994.3620.03720.12430.08930.0714-0.08720.039-0.0859-0.36720.01940.1597-0.0029-0.01630.1089-0.03150.159121.594369.298219.0947
52.6877-1.95390.72823.9277-0.62641.9271-0.0248-0.1241-0.04090.208-0.01310.1375-0.1819-0.19260.06140.1181-0.00180.02720.1242-0.01350.091620.524675.985223.6972
67.5341-4.50952.67523.0616-2.9114.6085-0.1022-0.4424-0.73980.02010.34210.59910.3585-0.4072-0.13280.1667-0.05220.04480.17430.00110.17316.716667.596225.1133
75.1489-2.15772.22022.6424-1.74094.548-0.06070.20930.2013-0.06260.01210.0886-0.4905-0.33160.05220.16310.04070.00550.11040.00440.116923.496177.47216.4713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:20)
2X-RAY DIFFRACTION2(chain A and resseq 21:59)
3X-RAY DIFFRACTION3(chain A and resseq 60:86)
4X-RAY DIFFRACTION4(chain A and resseq 87:107)
5X-RAY DIFFRACTION5(chain A and resseq 108:143)
6X-RAY DIFFRACTION6(chain A and resseq 144:172)
7X-RAY DIFFRACTION7(chain A and resseq 173:203)

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