4M7E | pdb_00004m7e

Structural insight into BL-induced activation of the BRI1-BAK1 complex

PDB DOI: https://doi.org/10.2210/pdb4M7E/pdb

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Mutation(s): No

Deposited: 2013-08-12 Released: 2013-10-16
Deposition Author(s): Chai, J., Han, Z., Sun, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free:
0.275 (Depositor), 0.280 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.223 (Depositor)

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 insight into BL-induced activation of the BRI1-BAK1 complex

Sun, Y., Han, Z., Chai, J.

To be published.

Macromolecule Content

Total Structure Weight: 212.86 kDa
Atom Count: 13,926
Modeled Residue Count: 1,817
Deposited Residue Count: 1,936
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BRASSINOSTEROID INSENSITIVE 1	A, B	767	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BRI1, At4g39400, F23K16.30 EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for O22476 (Arabidopsis thaliana) Explore O22476 Go to UniProtKB: O22476
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O22476
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1	C [auth D], D [auth C]	201	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BAK1, ELG, SERK3, At4g33430, F17M5.190 EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for Q94F62 (Arabidopsis thaliana) Explore Q94F62 Go to UniProtKB: Q94F62
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q94F62
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLD Query on BLD Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B]	L [auth A], O [auth B]	Brassinolide C₂₈ H₄₈ O₆ IXVMHGVQKLDRKH-KNBKMWSGSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Interactions & Density Focus chain L [auth A] Focus chain O [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B]	I [auth A], J [auth A], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B]	K [auth A], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain N [auth B] Interactions & Density Focus chain K [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.275 (Depositor), 0.280 (DCC)
R-Value Work: 0.220 (Depositor), 0.220 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.911	α = 90
b = 145.911	β = 90
c = 166.24	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-10-16

Deposition Author(s):

Chai, J.

Han, Z.

Sun, Y.

Revision History (Full details and data files)

Version 1.0: 2013-10-16
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary