7A0J | pdb_00007a0j

Crystal structure of the CRINKLY WD40 ectodomain from the Arabidopsis thaliana receptor kinase ACR4

PDB DOI: https://doi.org/10.2210/pdb7A0J/pdb

Classification: SIGNALING PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2020-08-09 Released: 2021-08-18
Deposition Author(s): Hothorn, M., Okuda, S.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.239 (Depositor), 0.241 (DCC)
R-Value Work:
0.220 (Depositor), 0.223 (DCC)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structures of Arabidopsis and Physcomitrella CR4 reveal the molecular architecture of CRINKLY4 receptor kinases.

Okuda, S., Hothorn, L.A., Hothorn, M.

To be published.

Macromolecule Content

Total Structure Weight: 136.41 kDa
Atom Count: 8,356
Modeled Residue Count: 1,089
Deposited Residue Count: 1,248
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase-like protein ACR4	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	312	Arabidopsis thaliana	Mutation(s): 0 Gene Names: ACR4, At3g59420, F25L23.280 EC: 2.7.11.1
UniProt
Find proteins for Q9LX29 (Arabidopsis thaliana) Explore Q9LX29 Go to UniProtKB: Q9LX29
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LX29
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth BBB] Focus chain C [auth CCC] Focus chain D [auth DDD]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth BaB], F [auth CcC]	2		N-Glycosylation	Interactions Focus chain E [auth BaB] Focus chain F [auth CcC] Interactions & Density Focus chain E [auth BaB] Focus chain F [auth CcC]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Q [auth DDD] MOL2 format, chain Q [auth DDD] mmCIF format, chain Q [auth DDD]	Q [auth DDD]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Q [auth DDD] Interactions & Density Focus chain Q [auth DDD]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain R [auth DDD] SDF format, chain P [auth CCC] SDF format, chain O [auth CCC] SDF format, chain N [auth CCC] SDF format, chain M [auth CCC] SDF format, chain L [auth CCC] SDF format, chain K [auth CCC] SDF format, chain J [auth CCC] SDF format, chain I [auth CCC] SDF format, chain H [auth AAA] SDF format, chain G [auth AAA] MOL2 format, chain R [auth DDD] MOL2 format, chain P [auth CCC] MOL2 format, chain O [auth CCC] MOL2 format, chain N [auth CCC] MOL2 format, chain M [auth CCC] MOL2 format, chain L [auth CCC] MOL2 format, chain K [auth CCC] MOL2 format, chain J [auth CCC] MOL2 format, chain I [auth CCC] MOL2 format, chain H [auth AAA] MOL2 format, chain G [auth AAA] mmCIF format, chain R [auth DDD] mmCIF format, chain P [auth CCC] mmCIF format, chain O [auth CCC] mmCIF format, chain N [auth CCC] mmCIF format, chain M [auth CCC] mmCIF format, chain L [auth CCC] mmCIF format, chain K [auth CCC] mmCIF format, chain J [auth CCC] mmCIF format, chain I [auth CCC] mmCIF format, chain H [auth AAA] mmCIF format, chain G [auth AAA]	G [auth AAA] H [auth AAA] I [auth CCC] J [auth CCC] K [auth CCC] G [auth AAA], H [auth AAA], I [auth CCC], J [auth CCC], K [auth CCC], L [auth CCC], M [auth CCC], N [auth CCC], O [auth CCC], P [auth CCC], R [auth DDD]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth CCC] Focus chain J [auth CCC] Focus chain K [auth CCC] Focus chain L [auth CCC] Focus chain M [auth CCC] Focus chain N [auth CCC] Focus chain O [auth CCC] Focus chain P [auth CCC] Focus chain R [auth DDD] Interactions & Density Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth CCC] Focus chain J [auth CCC] Focus chain K [auth CCC] Focus chain L [auth CCC] Focus chain M [auth CCC] Focus chain N [auth CCC] Focus chain O [auth CCC] Focus chain P [auth CCC] Focus chain R [auth DDD]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.239 (Depositor), 0.241 (DCC)
R-Value Work: 0.220 (Depositor), 0.223 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.991	α = 90
b = 87.952	β = 90.097
c = 88.618	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
autoSHARP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A_176237
Swiss National Science Foundation	Switzerland	31CP30_180213

Revision History (Full details and data files)

Version 1.0: 2021-08-18
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Derived calculations, 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.