7PFP

Full-length cryo-EM structure of the native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament

• PDB DOI: https://doi.org/10.2210/pdb7PFP/pdb
• EM Map EMD-13378: EMDB EMDataResource

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2021-08-11 Released: 2022-03-16 
• Deposition Author(s): Jovine, L., Xu, C., Stsiapanava, A., Carroni, M., Tunyasuvunakool, K., Jumper, J., Wu, B.
• Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation, Ministry of Education (MoE, Singapore)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 224.8 kDa 
• Atom Count: 9,582 
• Modelled Residue Count: 1,127 
• Deposited Residue Count: 1,920 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uromodulin	A, B, C	640	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P07911 (Homo sapiens) Explore P07911  Go to UniProtKB:  P07911
PHAROS:  P07911 GTEx:  ENSG00000169344

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D, L	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, M	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, N	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G36191CD GlyCosmos:  G36191CD GlyGen:  G36191CD

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, O	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80966KZ GlyCosmos:  G80966KZ GlyGen:  G80966KZ

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H, P	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, Q	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G46638GC GlyCosmos:  G46638GC GlyGen:  G46638GC

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	J, K	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0.5
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Jovine, L., Xu, C., Stsiapanava, A., Carroni, M., Tunyasuvunakool, K., Jumper, J., Wu, B.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2016-03999
Swedish Research Council	Sweden	2020-04936
Knut and Alice Wallenberg Foundation	Sweden	2018.0042
Ministry of Education (MoE, Singapore)	Sweden	MOH-000382-00

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2022-03-23
  Changes: Database references
• Version 1.2: 2022-03-30
  Changes: Database references