255,630
Structures from the PDB archive

1,062,058
Computed Structure Models (CSM)

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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Ligand Structure Quality Assessment

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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.

State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.

Van Andel Research Institute, Grand Rapids, MI 49503, USA.

VARI-SIMM Center, CAS-Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

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	👁 Image
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

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| 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	👁 Image
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 H [auth D] SDF format, chain G [auth D] SDF format, chain F [auth C] SDF format, chain E [auth C] MOL2 format, chain H [auth D] MOL2 format, chain G [auth D] MOL2 format, chain F [auth C] MOL2 format, chain E [auth C] mmCIF format, chain H [auth D] mmCIF format, chain G [auth D] mmCIF format, chain F [auth C] mmCIF format, chain E [auth C]	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	👁 Image	Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth D] Focus chain H [auth D] 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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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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

URL: https://www.rcsb.org/structure/5CL1

⇱ RCSB PDB - 5CL1: Complex structure of Norrin with human Frizzled 4