6QAJ: Tripartite motif of KAP1/TRIM28

Structure of the tripartite motif of KAP1/TRIM28. Determined by X-ray diffraction at 2.9 Å resolution. Released 24 Jul 2019.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Enterobacteria phage T4, Homo sapiens
Chains: 2
Atoms: 6,963
Mol. weight: 123.47 kDa
Ligands: ZN
Released: 24 Jul 2019

Explore 6QAJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QAJ contains 41 α-helices and 36 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: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	-101--97	5
β-strand	-93--92	2	1
β-strand	-91	1	2
β-strand	-90--88	3	1
β-strand	-82--79	4	1
β-strand	-76--73	4	1
α-helix	-68--57	12
β-strand	-50	1	2
α-helix	-47--27	21
α-helix	-22--18	5
α-helix	-14--1	14
α-helix	1-4	4
α-helix	8-15	8
α-helix	19-26	8
α-helix	30-34	5
α-helix	36-48	13
α-helix	52-60	9
α-helix	61-63	3
β-strand	64	1	3
β-strand	71	1	3
β-strand	78-80	3	4
β-strand	86-88	3	4
β-strand	114-116	3	5
β-strand	123-125	3	5
β-strand	130	1	4
α-helix	207	1
β-strand	208	1	6
α-helix	209	1
β-strand	216	1	6
β-strand	219-221	3	7
β-strand	227-228	2	7
α-helix	230-235	6
β-strand	242-243	2	7
α-helix	245-349	105
α-helix	350-353	4
α-helix	358-361	4
α-helix	362-369	8
α-helix	379-383	5
α-helix	390-397	8

Chain B: 20 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	-103--97	7
β-strand	-93--92	2	8
β-strand	-91	1	9
β-strand	-90--88	3	8
β-strand	-82--79	4	8
β-strand	-76--73	4	8
α-helix	-68--57	12
β-strand	-50	1	9
α-helix	-47--27	21
α-helix	-22--18	5
α-helix	-14--1	14
α-helix	1-4	4
α-helix	8-15	8
α-helix	19-27	9
α-helix	30-34	5
α-helix	36-48	13
α-helix	52-61	10
β-strand	64	1	10
β-strand	71	1	10
α-helix	77-78	2
β-strand	79-80	2	11
β-strand	86-87	2	11
β-strand	115-116	2	12
β-strand	123-124	2	12
β-strand	130	1	11
α-helix	207	1
β-strand	208	1	13
α-helix	209	1
β-strand	216	1	13
β-strand	217-220	4	14
β-strand	227-229	3	14
α-helix	230-235	6
β-strand	244	1	14
α-helix	245-350	106
α-helix	351-353	3
α-helix	358-361	4
α-helix	362-369	8
α-helix	390-396	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endolysin,Transcription intermediary factor 1-beta	A, B	protein	544	Enterobacteria phage T4, Homo sapiens	P00720, Q13263 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6QAJ_1 Endolysin,Transcription intermediary factor 1-beta (chains A, B)
MGSSHHHHHHSQDPNSSSENLYFQGNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKS
PSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRR
CALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTG
TWDAYAAEALELLEHCGVCRERLRPEREPRLLPCLHSACSACLGPAAPAAANSSGDGGAA
GDGTVVDCPVCKQQCFSKDIVENYFMRDSGSKAATDAQDANQCCTSCEDNAPATSYCVEC
SEPLCETCVEAHQRVKYTKDHTVRSTGPAKSRDGERTVYCNVHKHEPLVLFCESCDTLTC
RDCQLNAHKDHQYQFLEDAVRNQRKLLASLVKRLGDKHATLQKSTKEVRSSIRQVSDVQK
RVQVDVKMAILQIMKELNKRGRVLVNDAQKVTEGQQERLERQHWTMTKIQKHQEHILRFA
SWALESDNNTALLLSKKLIYFQLHRALKMIVDPVEPHGEMKFQWDLNAWTKSAEAFGKIV
AERP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing. Stoll, G.A., Oda, S.I., Chong, Z.S. et al. Proc Natl Acad Sci U S A (2019) 116:15042-15051. DOI 10.1073/pnas.1901318116 · PubMed

Other PDB entries of the same protein (UniProt P00720), best resolution first:

2O7A 0.84 Å, T4 lysozyme C-terminal fragment
5JDT 1.0 Å, Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K
7LOE 1.01 Å, T4 lysozyme mutant L99A in complex with 1-fluoranylnaphthalene
7LOD 1.02 Å, T4 lysozyme mutant L99A in complex with 1-fluoranyl-4-iodanyl-benzene
7LX8 1.03 Å, T4 lysozyme mutant L99A
5XPF 1.04 Å, High-resolution X-ray structure of the T26H mutant of T4 lysozyme
6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
7LOF 1.05 Å, T4 lysozyme mutant L99A in complex with 2-butylthiophene
7LX6 1.05 Å, T4 lysozyme mutant L99A
7LX7 1.05 Å, T4 lysozyme mutant L99A
1SWY 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure…
1SWZ 1.06 Å, Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure…

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