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- PDB-4hcr: Crystal structure of human MAdCAM-1 D1D2 complexed with Fab PF-547659 -

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Basic information

Entry
Database: PDB / ID: 4hcr
TitleCrystal structure of human MAdCAM-1 D1D2 complexed with Fab PF-547659
Components
  • Mucosal addressin cell adhesion molecule 1
  • PF-547659 heavy chain
  • PF-547659 light chain
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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details
Revision 1.2Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: PF-547659 heavy chain
L: PF-547659 light chain
A: Mucosal addressin cell adhesion molecule 1
M: PF-547659 heavy chain
N: PF-547659 light chain
B: Mucosal addressin cell adhesion molecule 1


Theoretical massNumber of molelcules
Total (without water)141,9976
Polymers141,9976
Non-polymers00
Water18,3031016
1
H: PF-547659 heavy chain
L: PF-547659 light chain
A: Mucosal addressin cell adhesion molecule 1


Theoretical massNumber of molelcules
Total (without water)70,9983
Polymers70,9983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: PF-547659 heavy chain
N: PF-547659 light chain
B: Mucosal addressin cell adhesion molecule 1


Theoretical massNumber of molelcules
Total (without water)70,9983
Polymers70,9983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.940, 112.260, 157.920
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody PF-547659 heavy chain


Mass: 24484.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody PF-547659 light chain


Mass: 24166.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Mucosal addressin cell adhesion molecule 1 / MAdCAM-1 / hMAdCAM-1


Mass: 22348.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MADCAM1 / Cell line (production host): HEK 293 GNTI(-) / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: Q13477
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1016 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Citrate pH 6.0, 18% (w/v) PEG 3350, 12% (w/v) myo-inositol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2011
RadiationMonochromator: double silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48 Å / Num. all: 59513 / Num. obs: 59513 / % possible obs: 96.1 % / 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
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.66 Å / σ(F): 1.99 / Phase error: 23.27 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2077 1048 1.76 %
Rwork0.1535 --
obs0.1578 59491 96.14 %
all-59491 -
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9498 0 0 1016 10514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019816
X-RAY DIFFRACTIONf_angle_d1.50413388
X-RAY DIFFRACTIONf_dihedral_angle_d13.9713538
X-RAY DIFFRACTIONf_chiral_restr0.0731542
X-RAY DIFFRACTIONf_plane_restr0.0091732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3008-2.42210.26161480.19828162X-RAY DIFFRACTION93
2.4221-2.57380.25871340.18728236X-RAY DIFFRACTION94
2.5738-2.77240.27891440.18358243X-RAY DIFFRACTION94
2.7724-3.05120.22311460.16978391X-RAY DIFFRACTION95
3.0512-3.49220.18351460.14598366X-RAY DIFFRACTION95
3.4922-4.3980.19841410.12848417X-RAY DIFFRACTION95
4.398-31.83310.18071510.14768588X-RAY DIFFRACTION96

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