6KKG | pdb_00006kkg

Crystal structure of MAGI2-Dendrin complex

PDB DOI: https://doi.org/10.2210/pdb6KKG/pdb

Classification: CELL ADHESION
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-07-25 Released: 2020-07-29
Deposition Author(s): Zhu, J.W., Zhang, H.J., Lin, L., Zhang, R.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.264 (Depositor), 0.228 (DCC)
R-Value Work:
0.202 (Depositor), 0.205 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6KKG

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

Literature

Phase separation of MAGI2-mediated complex underlies formation of slit diaphragm complex in glomerular filtration barrier

Zhang, H.J., Lin, L., Lin, Z.J., Liu, J.P., Pan, L.F., Zhang, M.J., Zhu, J.W., Zhang, R.G.

To be published.

Macromolecule Content

Total Structure Weight: 28.64 kDa
Atom Count: 1,917
Modeled Residue Count: 214
Deposited Residue Count: 248
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2	A, B	100	Mus musculus	Mutation(s): 0 Gene Names: Magi2, Acvrinp1, Aip1, Arip1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9WVQ1 (Mus musculus) Explore Q9WVQ1 Go to UniProtKB: Q9WVQ1
IMPC: MGI:1354953
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WVQ1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Dendrin	C, D	24	Mus musculus	Mutation(s): 0 Gene Names: Ddn, Gm748, Kiaa0749
UniProt
Find proteins for Q80TS7 (Mus musculus) Explore Q80TS7 Go to UniProtKB: Q80TS7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q80TS7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.264 (Depositor), 0.228 (DCC)
R-Value Work: 0.202 (Depositor), 0.205 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.715	α = 90
b = 55.715	β = 90
c = 74.696	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-07-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-07-29
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description