4WRN

Crystal structure of the polymerization region of human uromodulin/Tamm-Horsfall protein

• PDB DOI: https://doi.org/10.2210/pdb4WRN/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Escherichia coli O157:H7, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2014-10-24 Released: 2016-01-27 
• Deposition Author(s): Bokhove, M., De Sanctis, D., Jovine, L.
• Funding Organization(s): Karolinska Institutet, Center for Biosciences, Swedish Research Council, Gustafsson Foundation for Research in Natural Sciences and Medicine, Sven and Ebba-Christina Hagberg foundation, European Molecular Biology Organization, European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.246 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 154.56 kDa 
• Atom Count: 10,573 
• Modelled Residue Count: 1,356 
• Deposited Residue Count: 1,390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Uromodulin	A, B	695	Escherichia coli O157:H7, Homo sapiens This entity is chimeric	Mutation(s): 17  Gene Names: malE, Z5632, ECs5017, UMOD
UniProt & NIH Common Fund Data Resources
Find proteins for P07911 (Homo sapiens) Explore P07911  Go to UniProtKB:  P07911
PHAROS:  P07911 GTEx:  ENSG00000169344
Find proteins for P0AEY0 (Escherichia coli O157:H7) Explore P0AEY0  Go to UniProtKB:  P0AEY0
UniProt Groups	P07911P0AEY0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A], I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	G [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.246 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.32	α = 90
b = 242.32	β = 90
c = 258.86	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Bokhove, M., De Sanctis, D., Jovine, L.

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Funding Organization	Location	Grant Number
Karolinska Institutet	Sweden	--
Center for Biosciences	Sweden	--
Swedish Research Council	Sweden	2012-5093
Gustafsson Foundation for Research in Natural Sciences and Medicine	Sweden	--
Sven and Ebba-Christina Hagberg foundation	Sweden	--
European Molecular Biology Organization		--
European Union		ERC 260759

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2016-02-10
  Changes: Database references
• Version 1.2: 2016-02-17
  Changes: Database references
• Version 1.3: 2017-09-06
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary