5EIU: Mini TRIM5 B-box 2 dimer C2 crystal form

Mini TRIM5 B-box 2 dimer C2 crystal form. Determined by X-ray diffraction at 1.91 Å resolution. Released 15 Jun 2016.

Method: X-ray diffraction
Resolution: 1.91 Å
Organisms: Macaca mulatta, Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Chains: 2
Atoms: 2,264
Mol. weight: 33.21 kDa
Ligands: ZN
Released: 15 Jun 2016

Explore 5EIU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EIU contains 11 α-helices and 10 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	96	1	1
β-strand	103	1	1
β-strand	106-108	3	2
β-strand	113-115	3	2
α-helix	117-121	5
β-strand	130-132	3	2
α-helix	133-171	39
α-helix	174-206	33
α-helix	209-213	5
α-helix	216-227	12

Chain D: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	96	1	3
β-strand	103	1	3
β-strand	106-108	3	4
β-strand	113-115	3	4
α-helix	117-120	4
α-helix	123-125	3
β-strand	130-132	3	4
α-helix	133-168	36
α-helix	174-206	33
α-helix	209-213	5
α-helix	216-224	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TRIM protein-E3 ligase Chimera	A, D	protein	141	Macaca mulatta, Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	P34945 (AlphaFold model), Q0PF16 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5EIU_1 TRIM protein-E3 ligase Chimera (chains A, D)
EEGQKVDHCARHGEKLLLFCQEDSKVICWLCERSQEHRGHHTFLMEEVAQEYHVKLQTAL
EMLRQKQQEAETERNQVAKRVPKAPPEEKEALIARGKALGEQTQYMRELISELEHRLQGS
MMDLLQGVDGIIKRIENMTLK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5 alpha. Wagner, J.M., Roganowicz, M.D., Skorupka, K. et al. Elife (2016) 5. DOI 10.7554/eLife.16309 · PubMed

Other PDB entries of the same protein (UniProt P34945 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5F7T 2.29 Å, TRIM5 B-box2 and coiled-coil chimera
5VA4 2.31 Å, TRIM-Cyclophilin A B-box 2 and coiled-coil chimera
1SES 2.5 Å, Crystal structures at 2.5 Å resolution of seryl-tRNA synthetase complexed with two…
1SRY 2.5 Å, Refined crystal structure of the seryl-tRNA synthetase from thermus thermophilus at 2.5…
1SET 2.55 Å, Crystal structures at 2.5 Å resolution of seryl-tRNA synthetase complexed with two…
9QRP 2.7 Å, Thermus thermophilus seryl-tRNA synthetase bound to tRNA(ser)(GGA) and seryl-adenylate…
1SER 2.9 Å, The 2.9 Å crystal structure of T. Thermophilus seryl-tRNA synthetase complexed with tRNA…
5IEA 3.26 Å, TRIM5 B-box2 and coiled-coil chimera

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