5HZ0 | pdb_00005hz0

Plant peptide hormone receptor RGFR1 in complex with RGF2

• PDB DOI: https://doi.org/10.2210/pdb5HZ0/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana, Arabidopsis
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): Yes 


• Deposited: 2016-02-02 Released: 2017-04-05 
• Deposition Author(s): Song, W., Han, Z., Chai, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 
  0.264 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Plant Receptor

Song, W., Han, Z., Chai, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.89 kDa 
• Atom Count: 4,954 
• Modeled Residue Count: 637 
• Deposited Residue Count: 646 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable LRR receptor-like serine/threonine-protein kinase At4g26540	A [auth B]	633	Arabidopsis thaliana	Mutation(s): 5  Gene Names: At4g26540, M3E9.30 EC: 2.7.11.1
UniProt
Find proteins for C0LGR3 (Arabidopsis thaliana) Explore C0LGR3  Go to UniProtKB:  C0LGR3
Glycosylation
Glycosylation Sites: 3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ASP-PTR-TRP-LYS-PRO-ARG-HIS-HIS-PRO-HYP-ARG-ASN-ASN	B [auth A]	13	Arabidopsis	Mutation(s): 0
UniProt
Find proteins for Q6DSU1 (Arabidopsis thaliana) Explore Q6DSU1  Go to UniProtKB:  Q6DSU1

Oligosaccharides

Help  

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth B], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HZP	B [auth A]	L-PEPTIDE LINKING	C5 H9 N O3		PRO
PTR	B [auth A]	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free:  0.264 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181	α = 90
b = 181	β = 90
c = 87.968	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Song, W., Han, Z., Chai, J.

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2025-04-09
  Changes: Data collection, Database references, Structure summary