› 6q5y

X-ray diffraction
2.85Å resolution

Crystal structure of the SPOC domain of human PHF3 in complex with RNA polymerase II CTD diheptapeptide phosphorylated on Ser2Ser5

Released:
DOI: 10.2210/pdb6q5y/pdb
PDB entry 6q5y coloured by chain, front view.
PDB entry 6q5y coloured by chain, side view.
PDB entry 6q5y coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC
Appel LM, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D
Nat Commun 12 6078- (2021)

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assemblies composition:
monomeric
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150304 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
PHD finger protein 3 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 162 amino acids
Theoretical weight: 18.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q92576 (Residues: 1199-1356; Coverage: 8%)
Gene names: KIAA0244, PHF3
Sequence domains: SPOC domain
DNA-directed RNA polymerase II subunit RPB1 Chains: E, F
Molecule details ›
Chains: E, F
Length: 14 amino acids
Theoretical weight: 1.78 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P24928 (Residues: 1790-1803; Coverage: 1%)
Gene names: POLR2, POLR2A
Sequence domains: RNA polymerase Rpb1 C-terminal repeat

Ligands and Environments

No bound ligands
1 modified residue:
Ligand SEP 8 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P32
Unit cell:
a: 67.832Å b: 67.832Å c: 178.118Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.194 0.192 0.227
Expression systems:
  • Escherichia coli
  • Not provided

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