5E6S | pdb_00005e6s

Structures of leukocyte integrin aLB2: The aI domain, the headpiece, and the pocket for the internal ligand

  • Classification: CELL ADHESION
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2015-10-10 Released: 2016-03-02 
  • Deposition Author(s): Springer, T.A., Sen, M.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.234 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history

Literature

Leukocyte integrin alpha L beta 2 headpiece structures: The alpha I domain, the pocket for the internal ligand, and concerted movements of its loops.

Sen, M.Springer, T.A.

(2016) Proc Natl Acad Sci U S A 113: 2940-2945

  • DOI: https://doi.org/10.1073/pnas.1601379113
  • Primary Citation Related Structures: 
    5E6R, 5E6S, 5E6U, 5E6V, 5E6W, 5E6X, 5ES4

  • PubMed Abstract: 

    High-resolution crystal structures of the headpiece of lymphocyte function-associated antigen-1 (integrin αLβ2) reveal how the αI domain interacts with its platform formed by the α-subunit β-propeller and β-subunit βI domains. The αLβ2 structures compared with αXβ2 structures show that the αI domain, tethered through its N-linker and a disulfide to a stable β-ribbon pillar near the center of the platform, can undergo remarkable pivoting and tilting motions that appear buffered by N-glycan decorations that differ between αL and αX subunits. Rerefined β2 integrin structures reveal details including pyroglutamic acid at the β2 N terminus and bending within the EGF1 domain. Allostery is relayed to the αI domain by an internal ligand that binds to a pocket at the interface between the β-propeller and βI domains. Marked differences between the αL and αX subunit β-propeller domains concentrate near the binding pocket and αI domain interfaces. Remarkably, movement in allostery in the βI domain of specificity determining loop 1 (SDL1) causes concerted movement of SDL2 and thereby tightens the binding pocket for the internal ligand.


  • Organizational Affiliation
    • Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA 02115; Department of Biology and Biochemistry, University of Houston, Houston, TX 77204.

Macromolecule Content 

  • Total Structure Weight: 436.89 kDa 
  • Atom Count: 26,342 
  • Modeled Residue Count: 3,102 
  • Deposited Residue Count: 3,915 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin alpha-L
A, C, E
795Homo sapiensMutation(s): 3 
Gene Names: ITGALCD11A
UniProt & NIH Common Fund Data Resources
Find proteins for P20701 (Homo sapiens)
Explore P20701 
Go to UniProtKB:  P20701
PHAROS:  P20701
GTEx:  ENSG00000005844 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20701
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P20701-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Integrin beta-2
B, D, F
510Homo sapiensMutation(s): 1 
Gene Names: ITGB2CD18MFI7
UniProt & NIH Common Fund Data Resources
Find proteins for P05107 (Homo sapiens)
Explore P05107 
Go to UniProtKB:  P05107
PHAROS:  P05107
GTEx:  ENSG00000160255 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05107
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P05107-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
CA [auth E]
FA [auth F]
GA [auth F]
K [auth A]
N [auth B]
CA [auth E],
FA [auth F],
GA [auth F],
K [auth A],
N [auth B],
O [auth B],
T [auth C],
W [auth D],
X [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AA [auth E]
BA [auth E]
DA [auth F]
EA [auth F]
H [auth A]
AA [auth E],
BA [auth E],
DA [auth F],
EA [auth F],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
Q [auth C],
R [auth C],
S [auth C],
U [auth D],
V [auth D],
Z [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
P [auth C],
Y [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.9α = 90
b = 118.877β = 118.52
c = 150.967γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesNCI CA031798

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2016-05-11
    Changes: Database references
  • Version 1.3: 2016-07-20
    Changes: Data collection
  • Version 1.4: 2017-09-27
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.5: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.7: 2024-11-06
    Changes: Data collection, Database references, Structure summary