7JUB

C-type carbohydrate-recognition domain 4 of the mannose receptor complexed with methyl-mannoside

• PDB DOI: https://doi.org/10.2210/pdb7JUB/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-08-19 Released: 2021-02-03 
• Deposition Author(s): Weis, W.I., Feinberg, H.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.157 
• R-Value Work: 0.134 
• R-Value Observed: 0.135 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.73 kDa 
• Atom Count: 1,258 
• Modelled Residue Count: 122 
• Deposited Residue Count: 135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage mannose receptor 1	A	135	Homo sapiens	Mutation(s): 0  Gene Names: MRC1, CLEC13D, CLEC13DL, MRC1L1
UniProt & NIH Common Fund Data Resources
Find proteins for P22897 (Homo sapiens) Explore P22897  Go to UniProtKB:  P22897
PHAROS:  P22897 GTEx:  ENSG00000260314

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMA	C [auth A]	methyl alpha-D-mannopyranoside C7 H14 O6 HOVAGTYPODGVJG-VEIUFWFVSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.157 
• R-Value Work: 0.134 
• R-Value Observed: 0.135 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.97	α = 90
b = 56.361	β = 112.01
c = 34.217	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Weis, W.I., Feinberg, H.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/P005659/1

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2021-02-17
  Changes: Database references
• Version 1.2: 2021-07-14
  Changes: Database references
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Refinement description