3V4P

crystal structure of a4b7 headpiece complexed with Fab ACT-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

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This is version 2.0 of the entry. See complete history


Literature

Structural specializations of a4b7, an Integrin that Mediates Rolling Adhesion

Yu, Y.Zhu, J.Mi, L.Z.Walz, T.Sun, H.Chen, J.Springer, T.A.

(2012) J Cell Biol 196: 131-146

  • DOI: https://doi.org/10.1083/jcb.201110023
  • Primary Citation of Related Structures:  
    3V4P, 3V4V

  • PubMed Abstract: 

    The lymphocyte homing receptor integrin α(4)β(7) is unusual for its ability to mediate both rolling and firm adhesion. α(4)β(1) and α(4)β(7) are targeted by therapeutics approved for multiple sclerosis and Crohn's disease. Here, we show by electron microscopy and crystallography how two therapeutic Fabs, a small molecule (RO0505376), and mucosal adhesion molecule-1 (MAdCAM-1) bind α(4)β(7). A long binding groove at the α(4)-β(7) interface for immunoglobulin superfamily domains differs in shape from integrin pockets that bind Arg-Gly-Asp motifs. RO0505376 mimics an Ile/Leu-Asp motif in α(4) ligands, and orients differently from Arg-Gly-Asp mimics. A novel auxiliary residue at the metal ion-dependent adhesion site in α(4)β(7) is essential for binding to MAdCAM-1 in Mg(2+) yet swings away when RO0505376 binds. A novel intermediate conformation of the α(4)β(7) headpiece binds MAdCAM-1 and supports rolling adhesion. Lack of induction of the open headpiece conformation by ligand binding enables rolling adhesion to persist until integrin activation is signaled.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Immune Disease Institute and Children's Hospital, Boston, MA 02115, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-4
A, C
597Homo sapiensMutation(s): 1 
Gene Names: ITGA4CD49D
UniProt & NIH Common Fund Data Resources
Find proteins for P13612 (Homo sapiens)
Explore P13612 
Go to UniProtKB:  P13612
PHAROS:  P13612
GTEx:  ENSG00000115232 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13612
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin beta-7
B, D
503Homo sapiensMutation(s): 0 
Gene Names: ITGB7
UniProt & NIH Common Fund Data Resources
Find proteins for P26010 (Homo sapiens)
Explore P26010 
Go to UniProtKB:  P26010
PHAROS:  P26010
GTEx:  ENSG00000139626 
Entity Groups  
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UniProt GroupP26010
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MONOCLONAL ANTIBODY Act-1 HEAVY CHAINE [auth H],
G [auth M]
219Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
MONOCLONAL ANTIBODY Act-1 LIGHT CHAINF [auth L],
H [auth N]
217Mus musculusMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth E],
J [auth F]
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
15P
Query on 15P

Download Ideal Coordinates CCD File 
R [auth A]POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
NAG
Query on NAG

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AA [auth C]
BA [auth C]
CA [auth C]
N [auth A]
O [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
V [auth B],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
DA [auth C]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
CA
Query on CA

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FA [auth D]
GA [auth D]
K [auth A]
L [auth A]
M [auth A]
FA [auth D],
GA [auth D],
K [auth A],
L [auth A],
M [auth A],
T [auth B],
U [auth B],
W [auth C],
X [auth C],
Y [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
EA [auth D],
S [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.78α = 90
b = 122.74β = 115.38
c = 158.14γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary