5CL1 | pdb_00005cl1

Complex structure of Norrin with human Frizzled 4

PDB DOI: https://doi.org/10.2210/pdb5CL1/pdb

Classification: SIGNALING PROTEIN
Organism(s): Escherichia coli O157:H7, Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2015-07-16 Released: 2015-08-12
Deposition Author(s): Wang, Z., Ke, J., Shen, G., Cheng, Z., Xu, H.E., Xu, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free:
0.310 (Depositor), 0.304 (DCC)
R-Value Work:
0.262 (Depositor), 0.263 (DCC)
R-Value Observed:
0.264 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/cr.2015.92
Primary Citation Related Structures:
5CL1, 5CM4

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 138.41 kDa
Atom Count: 9,227
Modeled Residue Count: 1,177
Deposited Residue Count: 1,228
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Norrin	A, B	483	Escherichia coli O157:H7, Homo sapiens This entity is chimeric	Mutation(s): 0 Gene Names: malE, Z5632, ECs5017, NDP, EVR2
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEY0 (Escherichia coli O157:H7) Explore P0AEY0 Go to UniProtKB: P0AEY0
Find proteins for Q00604 (Homo sapiens) Explore Q00604 Go to UniProtKB: Q00604
PHAROS: Q00604 GTEx: ENSG00000124479
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P0AEY0 Q00604
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Frizzled-4	C, D	131	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ULV1
Sequence Annotations Expand
Reference Sequence

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 E [auth C] SDF format, chain F [auth C] SDF format, chain G [auth D] SDF format, chain H [auth D] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth D] MOL2 format, chain H [auth D] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain G [auth D] mmCIF format, chain H [auth D]	E [auth C], F [auth C], G [auth D], H [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth D] Focus chain H [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth D] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free: 0.310 (Depositor), 0.304 (DCC)
R-Value Work: 0.262 (Depositor), 0.263 (DCC)
R-Value Observed: 0.264 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.291	α = 90
b = 150.589	β = 90
c = 92.32	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

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: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2024-10-16
Changes: Structure summary