2OX8 | pdb_00002ox8

Human Scavenger Receptor C-type Lectin carbohydrate-recognition domain.

PDB DOI: https://doi.org/10.2210/pdb2OX8/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-02-20 Released: 2007-04-03
Deposition Author(s): Weis, W.I., Feinberg, H., Drickamer, K., Taylor, M.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.308 (Depositor), 0.309 (DCC)
R-Value Work:
0.233 (Depositor), 0.236 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Scavenger receptor C-type lectin binds to the leukocyte cell surface glycan Lewis(x) by a novel mechanism.

Feinberg, H., Taylor, M.E., Weis, W.I.

(2007) J Biological Chem 282: 17250-17258

PubMed: 17420244 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M701624200
Primary Citation Related Structures:
2OX8, 2OX9

PubMed Abstract:
The scavenger receptor C-type lectin (SRCL) is unique in the family of class A scavenger receptors, because in addition to binding sites for oxidized lipoproteins it also contains a C-type carbohydrate-recognition domain (CRD) that interacts with specific glycans. Both human and mouse SRCL are highly specific for the Lewis(x) trisaccharide, which is commonly found on the surfaces of leukocytes and some tumor cells. Structural analysis of the CRD of mouse SRCL in complex with Lewis(x) and mutagenesis show the basis for this specificity. The interaction between mouse SRCL and Lewis(x) is analogous to the way that selectins and DC-SIGN bind to related fucosylated glycans, but the mechanism of the interaction is novel, because it is based on a primary galactose-binding site similar to the binding site in the asialoglycoprotein receptor. Crystals of the human receptor lacking bound calcium ions reveal an alternative conformation in which a glycan ligand would be released during receptor-mediated endocytosis.

Organizational Affiliation

Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94306, USA.

Macromolecule Content

Total Structure Weight: 67.56 kDa
Atom Count: 4,379
Modeled Residue Count: 516
Deposited Residue Count: 560
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Scavenger receptor with C-type lectin type I	A, B, C, D	140	Homo sapiens	Mutation(s): 0 Gene Names: SRCL
UniProt & NIH Common Fund Data Resources
Find proteins for Q5KU26 (Homo sapiens) Explore Q5KU26 Go to UniProtKB: Q5KU26
PHAROS: Q5KU26 GTEx: ENSG00000158270
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5KU26
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	CA [auth C] DA [auth D] E [auth A] EA [auth D] F [auth A] CA [auth C], DA [auth D], E [auth A], EA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], LA [auth D], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], U [auth C], V [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain LA [auth D] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain LA [auth D] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth C] IA [auth D] JA [auth D] KA [auth D] AA [auth C], BA [auth C], IA [auth D], JA [auth D], KA [auth D], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain Z [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	FA [auth D] GA [auth D] HA [auth D] J [auth A] K [auth A] FA [auth D], GA [auth D], HA [auth D], J [auth A], K [auth A], L [auth A], R [auth B], S [auth B], T [auth B], W [auth C], X [auth C], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.308 (Depositor), 0.309 (DCC)
R-Value Work: 0.233 (Depositor), 0.236 (DCC)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.422	α = 90
b = 80.422	β = 90
c = 67.159	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
Blu-Ice	data collection
COMO	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-04-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-04-03
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary