3K6S | pdb_00003k6s

Structure of integrin alphaXbeta2 ectodomain


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp3.50 Å
  • R-Value Free:&nbsp
    0.335 (Depositor), 0.311 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.297 (Depositor), 0.281 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.297&nbsp(Depositor)&nbsp

wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


Ligand Structure Quality Assessment&nbsp


This is version 2.1 of the entry. See complete&nbsphistory.&nbsp

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5ES4


Literature

Structure of an integrin with an alphaI domain, complement receptor type 4.

Xie, C.,&nbspZhu, J.,&nbspChen, X.,&nbspMi, L.,&nbspNishida, N.,&nbspSpringer, T.A.

(2010) EMBO J&nbsp29: 666-679

  • DOI:&nbsphttps://doi.org/10.1038/emboj.2009.367
  • Primary Citation of Related Structures: &nbsp
    3K6S, 3K71, 3K72

  • PubMed Abstract:&nbsp

    We report the structure of an integrin with an alphaI domain, alpha(X)beta(2), the complement receptor type 4. It was earlier expected that a fixed orientation between the alphaI domain and the beta-propeller domain in which it is inserted would be required for allosteric signal transmission. However, the alphaI domain is highly flexible, enabling two betaI domain conformational states to couple to three alphaI domain states, and greater accessibility for ligand recognition. Although alpha(X)beta(2) is bent similarly to integrins that lack alphaI domains, the terminal domains of the alpha- and beta-legs, calf-2 and beta-tail, are oriented differently than in alphaI-less integrins. Linkers extending to the transmembrane domains are unstructured. Previous mutations in the beta(2)-tail domain support the importance of extension, rather than a deadbolt, in integrin activation. The locations of further activating mutations and antibody epitopes show the critical role of extension, and conversion from the closed to the open headpiece conformation, in integrin activation. Differences among 10 molecules in crystal lattices provide unprecedented information on interdomain flexibility important for modelling integrin extension and activation.


  • Organizational Affiliation:&nbsp

    Department of Pathology, Harvard Medical School, Immune Disease Institute and Children's Hospital, Boston, MA 02115, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-X
A, C, E, G
1,095Homo sapiensMutation(s): 0&nbsp
Gene Names:&nbspCD11C,&nbspITGAX
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP20702&nbsp(Homo sapiens)
Explore&nbspP20702&nbsp
Go to UniProtKB: &nbspP20702
PHAROS: &nbspP20702
GTEx: &nbspENSG00000140678&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20702
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P20702-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin beta-2
B, D, F, H
687Homo sapiensMutation(s): 0&nbsp
Gene Names:&nbspCD18,&nbspITGB2,&nbspMFI7
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP05107&nbsp(Homo sapiens)
Explore&nbspP05107&nbsp
Go to UniProtKB: &nbspP05107
PHAROS: &nbspP05107
GTEx: &nbspENSG00000160255&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05107
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P05107-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, K, L, M, N
I, K, L, M, N, O, Q, R, T
2N-Glycosylation
Glycosylation Resources
GlyTouCan: &nbspG42666HT
GlyCosmos: &nbspG42666HT
GlyGen: &nbspG42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J
5N-Glycosylation
Glycosylation Resources
GlyTouCan: &nbspG21381MC
GlyCosmos: &nbspG21381MC
GlyGen: &nbspG21381MC
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
P, S
3N-Glycosylation
Glycosylation Resources
GlyTouCan: &nbspG62182OO
GlyCosmos: &nbspG62182OO
GlyGen: &nbspG62182OO
Small Molecules
Ligands&nbsp4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File&nbsp
BA [auth B]
DA [auth C]
EA [auth C]
IA [auth D]
KA [auth E]
BA [auth B],
DA [auth C],
EA [auth C],
IA [auth D],
KA [auth E],
LA [auth E],
PA [auth F],
RA [auth G],
SA [auth G],
V [auth A],
W [auth A],
WA [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File&nbsp
U [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
CA
Query on CA

Download Ideal Coordinates CCD File&nbsp
CA [auth B]
FA [auth C]
GA [auth C]
HA [auth C]
JA [auth D]
CA [auth B],
FA [auth C],
GA [auth C],
HA [auth C],
JA [auth D],
MA [auth E],
NA [auth E],
OA [auth E],
QA [auth F],
TA [auth G],
UA [auth G],
VA [auth G],
X [auth A],
XA [auth H],
Y [auth A],
Z [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File&nbsp
AA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp3.50 Å
  • R-Value Free:&nbsp 0.335 (Depositor), 0.311 (DCC)&nbsp
  • R-Value Work:&nbsp 0.297 (Depositor), 0.281 (DCC)&nbsp
  • R-Value Observed:&nbsp0.297&nbsp(Depositor)&nbsp
Space Group:&nbspP 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.095α = 90
b = 163.561β = 90
c = 536.911γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
SOLVEphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View&nbspFull Validation Report



Ligand Structure Quality Assessment&nbsp


Entry History&nbsp

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-12-13
    Changes: Advisory, Source and taxonomy
  • Version 1.3: 2018-06-20
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary