7PFP | pdb_00007pfp

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)

Experimental Data Snapshot

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

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH.

Stsiapanava, A., Xu, C., Nishio, S., Han, L., Yamakawa, N., Carroni, M., Tunyasuvunakool, K., Jumper, J., de Sanctis, D., Wu, B., Jovine, L.

(2022) Nat Struct Mol Biol 29: 190-193

PubMed: 35273390 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-022-00729-3
Primary Citation Related Structures:
7P6R, 7P6S, 7P6T, 7PFP, 7Q3N

PubMed Abstract:
Glycoprotein 2 (GP2) and uromodulin (UMOD) filaments protect against gastrointestinal and urinary tract infections by acting as decoys for bacterial fimbrial lectin FimH. By combining AlphaFold2 predictions with X-ray crystallography and cryo-EM, we show that these proteins contain a bipartite decoy module whose new fold presents the high-mannose glycan recognized by FimH. The structure rationalizes UMOD mutations associated with kidney diseases and visualizes a key epitope implicated in cast nephropathy.

Organizational Affiliation

Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07911
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P07911-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain D Focus chain L Interactions & Density Focus chain D Focus chain L
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain E Focus chain M Interactions & Density Focus chain E Focus chain M
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain F Focus chain N Interactions & Density Focus chain F Focus chain N
Glycosylation Resources
GlyTouCan: G36191CD GlyCosmos: G36191CD GlyGen: G36191CD

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain G Focus chain O Interactions & Density Focus chain G Focus chain O
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain H Focus chain P Interactions & Density Focus chain H Focus chain P
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain I Focus chain Q Interactions & Density Focus chain I Focus chain Q
Glycosylation Resources
GlyTouCan: G46638GC GlyCosmos: G46638GC GlyGen: G46638GC

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain J Focus chain K Interactions & Density Focus chain J Focus chain K
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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-16

Deposition Author(s):

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 (Full details and data files)

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
Version 1.3: 2024-10-16
Changes: Data collection, Refinement description, Structure summary