9NXF | pdb_00009nxf

Crystal structure of CN:Tak1 complex

PDB DOI: https://doi.org/10.2210/pdb9NXF/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-03-25 Released: 2025-12-17
Deposition Author(s): Shirakawa, K.T., Parikh, T., Page, R., Peti, W.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.13 Å
R-Value Free:
0.295 (Depositor), 0.295 (DCC)
R-Value Work:
0.248 (Depositor), 0.248 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

CN:Tak1 complex explains CN substrate specificity

Shirakawa, K.T., Parikh, T., Page, R., Peti, W.

To be published.

Macromolecule Content

Total Structure Weight: 134.13 kDa
Atom Count: 8,795
Modeled Residue Count: 1,082
Deposited Residue Count: 1,158
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein phosphatase 3 catalytic subunit alpha	A, D	370	Homo sapiens	Mutation(s): 1 Gene Names: PPP3CA, CALNA, CNA EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q08209 (Homo sapiens) Explore Q08209 Go to UniProtKB: Q08209
PHAROS: Q08209 GTEx: ENSG00000138814
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08209
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcineurin subunit B type 1	B, E	156	Homo sapiens	Mutation(s): 0 Gene Names: PPP3R1, CNA2, CNB
UniProt & NIH Common Fund Data Resources
Find proteins for P63098 (Homo sapiens) Explore P63098 Go to UniProtKB: P63098
PHAROS: P63098 GTEx: ENSG00000221823
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63098
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IkB-like protein,Mitogen-activated protein kinase kinase kinase 7	C, F	53	Homo sapiens	Mutation(s): 2 Gene Names: A238L, Mal-047, 5EL, MAP3K7, TAK1 EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for O36972 (African swine fever virus (isolate Tick/Malawi/Lil 20-1/1983)) Explore O36972 Go to UniProtKB: O36972
Find proteins for O43318 (Homo sapiens) Explore O43318 Go to UniProtKB: O43318
PHAROS: O43318 GTEx: ENSG00000135341
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	O43318O36972
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth D] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth B]	H [auth A], M [auth B], P [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain P [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain P [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D] mmCIF format, chain O [auth D]	O [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth D] Interactions & Density Focus chain O [auth D]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth D]	G [auth A], N [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain N [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain Q [auth E] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain R [auth E] SDF format, chain L [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain R [auth E] MOL2 format, chain L [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain R [auth E] mmCIF format, chain L [auth B]	I [auth B] J [auth B] K [auth B] L [auth B] Q [auth E] I [auth B], J [auth B], K [auth B], L [auth B], Q [auth E], R [auth E], S [auth E], T [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2RX Query on 2RX	C, F	L-PEPTIDE LINKING	C₃ H₈ N O₅ P S		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.13 Å
R-Value Free: 0.295 (Depositor), 0.295 (DCC)
R-Value Work: 0.248 (Depositor), 0.248 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 224.079	α = 90
b = 49.585	β = 128.72
c = 158.895	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM144379
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01NS124666

Revision History (Full details and data files)

Version 1.0: 2025-12-17
Type: Initial release

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Help and Resources

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Crystal structure of CN:Tak1 complex

CN:Tak1 complex explains CN substrate specificity

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

9NXF | pdb_00009nxf