4H3K | pdb_00004h3k

Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA polymerase II CTD peptide phosphorylated at Ser-2, Ser-5 and Ser-7

PDB DOI: https://doi.org/10.2210/pdb4H3K/pdb

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

Deposited: 2012-09-13 Released: 2012-10-31
Deposition Author(s): Xiang, K., Tong, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.233 (Depositor), 0.233 (DCC)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

An unexpected binding mode for a Pol II CTD peptide phosphorylated at Ser7 in the active site of the CTD phosphatase Ssu72.

Xiang, K., Manley, J.L., Tong, L.

(2012) Genes Dev 26: 2265-2270

PubMed: 23070812 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1101/gad.198853.112
Primary Citation Related Structures:
4H3H, 4H3K

PubMed Abstract:
Ssu72, an RNA polymerase II C-terminal domain (CTD) phospho-Ser5 (pSer5) phosphatase, was recently reported to have pSer7 phosphatase activity as well. We report here the crystal structure of a ternary complex of the N-terminal domain of human symplekin, human Ssu72, and a 10-mer pSer7 CTD peptide. Surprisingly, the peptide is bound in the Ssu72 active site with its backbone running in the opposite direction compared with a pSer5 peptide. The pSer7 phosphatase activity of Ssu72 is ∼4000-fold lower than its pSer5 phosphatase activity toward a peptide substrate, consistent with the structural observations.

Organizational Affiliation

Department of Biological Sciences, Columbia University, New York, New York 10027, USA.

Macromolecule Content

Total Structure Weight: 130.22 kDa
Atom Count: 8,247
Modeled Residue Count: 1,014
Deposited Residue Count: 1,140
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Symplekin	A, C [auth D]	351	Homo sapiens	Mutation(s): 0 Gene Names: SYMPK, SPK
UniProt & NIH Common Fund Data Resources
Find proteins for Q92797 (Homo sapiens) Explore Q92797 Go to UniProtKB: Q92797
PHAROS: Q92797 GTEx: ENSG00000125755
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92797
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II subunit A C-terminal domain phosphatase SSU72	B, D [auth E]	214	Homo sapiens	Mutation(s): 1 Gene Names: SSU72, HSPC182, PNAS-120 EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP77 (Homo sapiens) Explore Q9NP77 Go to UniProtKB: Q9NP77
PHAROS: Q9NP77 GTEx: ENSG00000160075
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NP77
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexapeptide	E [auth F]	10	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	E [auth F]	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.233 (Depositor), 0.233 (DCC)
R-Value Work: 0.197 (Depositor), 0.198 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.583	α = 90
b = 97.364	β = 97.86
c = 105.278	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-10-31

Deposition Author(s):

Xiang, K.

Tong, L.

Revision History (Full details and data files)

Version 1.0: 2012-10-31
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary