5CM4

Crystal structure of human Frizzled 4 Cysteine-Rich Domain (CRD)

PDB DOI: https://doi.org/10.2210/pdb5CM4/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2015-07-16 Released: 2015-08-12
Deposition Author(s): Ke, J., Parker, N., Gu, X., Zhang, C., Melcher, K., Xu, H.E.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.255
R-Value Work: 0.226
R-Value Observed: 0.227

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Structural basis of the Norrin-Frizzled 4 interaction.

Shen, G., Ke, J., Wang, Z., Cheng, Z., Gu, X., Wei, Y., Melcher, K., Xu, H.E., Xu, W.

(2015) Cell Res 25: 1078-1081

PubMed: 26227961 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/cr.2015.92
Primary Citation of Related Structures:
5CL1, 5CM4

Organizational Affiliation

Department of Biological Structure, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content

Total Structure Weight: 29.38 kDa
Atom Count: 1,998
Modelled Residue Count: 242
Deposited Residue Count: 250
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Frizzled-4	A, B	125	Homo sapiens	Mutation(s): 0 Gene Names: FZD4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULV1 (Homo sapiens) Explore Q9ULV1 Go to UniProtKB: Q9ULV1
PHAROS: Q9ULV1 GTEx: ENSG00000174804
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ULV1
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q9ULV1-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	D [auth A], E [auth B], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.255
R-Value Work: 0.226
R-Value Observed: 0.227
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.583	α = 90
b = 111.738	β = 90
c = 75.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK071662
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM102545
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM104212
Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor	United States	085P1000817

Revision History (Full details and data files)

Version 1.0: 2015-08-12
Type: Initial release
Version 1.1: 2015-09-16
Changes: Database references
Version 1.2: 2017-09-27
Changes: Author supporting evidence, Derived calculations
Version 1.3: 2019-12-25
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary