3HL2

The crystal structure of the human SepSecS-tRNASec complex

PDB DOI: https://doi.org/10.2210/pdb3HL2/pdb
NAKB: 3HL2

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-26 Released: 2009-10-06
Deposition Author(s): Palioura, S., Steitz, T.A., Soll, D., Simonovic, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.238
R-Value Work: 0.203
R-Value Observed: 0.203

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7MDL

Literature

The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation.

Palioura, S., Sherrer, R.L., Steitz, T.A., Soll, D., Simonovic, M.

(2009) Science 325: 321-325

PubMed: 19608919 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.1173755
Primary Citation of Related Structures:
3HL2

PubMed Abstract:
Selenocysteine is the only genetically encoded amino acid in humans whose biosynthesis occurs on its cognate transfer RNA (tRNA). O-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) catalyzes the final step of selenocysteine formation by a poorly understood tRNA-dependent mechanism. The crystal structure of human tRNA(Sec) in complex with SepSecS, phosphoserine, and thiophosphate, together with in vivo and in vitro enzyme assays, supports a pyridoxal phosphate-dependent mechanism of Sec-tRNA(Sec) formation. Two tRNA(Sec) molecules, with a fold distinct from other canonical tRNAs, bind to each SepSecS tetramer through their 13-base pair acceptor-TPsiC arm (where Psi indicates pseudouridine). The tRNA binding is likely to induce a conformational change in the enzyme's active site that allows a phosphoserine covalently attached to tRNA(Sec), but not free phosphoserine, to be oriented properly for the reaction to occur.

Organizational Affiliation

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Macromolecule Content

Total Structure Weight: 254.13 kDa
Atom Count: 17,628
Modelled Residue Count: 1,852
Deposited Residue Count: 2,094
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-phosphoseryl-tRNA(Sec) selenium transferase	A, B, C, D	501	Homo sapiens	Mutation(s): 0 Gene Names: SEPSECS, TRNP48 EC: 2.9.1.1 (PDB Primary Data), 2.9.1.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD40 (Homo sapiens) Explore Q9HD40 Go to UniProtKB: Q9HD40
PHAROS: Q9HD40 GTEx: ENSG00000109618
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HD40
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
tRNASec	E	90	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLR Query on PLR Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	F [auth A], I [auth B], L [auth C], N [auth D]	(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE C₈ H₁₂ N O₅ P RBCOYOYDYNXAFA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D]
SEP Query on SEP Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	J [auth B], K [auth B], O [auth D], P [auth D]	PHOSPHOSERINE C₃ H₈ N O₆ P BZQFBWGGLXLEPQ-REOHCLBHSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth D] Focus chain P [auth D]
TS6 Query on TS6 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth C]	G [auth A], H [auth A], M [auth C]	Monothiophosphate H₃ O₃ P S RYYWUUFWQRZTIU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.238
R-Value Work: 0.203
R-Value Observed: 0.203
Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.818	α = 90
b = 166.818	β = 90
c = 236.322	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	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: 2009-10-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-10-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description