6PI7: TDRD2 extended Tudor domain

Crystal structure of the TDRD2 extended Tudor domain in complex with an antibody fragment and the PIWIL1 peptide. Determined by X-ray diffraction at 2.8 Å resolution. Released 24 Jul 2019.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 7
Atoms: 8,998
Mol. weight: 153.61 kDa
Released: 24 Jul 2019

Explore 6PI7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PI7 contains 52 α-helices and 114 β-strands across 6 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.

Chains A and D: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	308-317	10	1
β-strand	320-325	6	1
α-helix	328-344	17
α-helix	347-349	3
β-strand	359-363	5	2
β-strand	370-378	9	2
α-helix	383	1
β-strand	384-388	5	2
β-strand	394-397	4	2
α-helix	399-401	3
β-strand	403	1	2
α-helix	407-410	4
α-helix	413-414	2
β-strand	417-421	5	1
β-strand	424-426	3	3
α-helix	433-443	11
β-strand	451-461	11	1
β-strand	464-473	10	1
β-strand	480-481	2	1
α-helix	482-488	7
β-strand	492-494	3	3
α-helix	495-496	2

Chain B: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	4
β-strand	11-14	4	5
β-strand	20-26	7	4
β-strand	34-39	6	5
β-strand	46-50	5	5
β-strand	54-55	2	5
α-helix	56	1
β-strand	63-68	6	4
β-strand	71-76	6	4
α-helix	81-83	3
β-strand	86-91	6	5
α-helix	97	1
β-strand	98-99	2	5
β-strand	103-107	5	5
β-strand	112	1	6
β-strand	115-119	5	7
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	7
β-strand	141	1	6
β-strand	146-151	6	8
β-strand	154-155	2	8
α-helix	156	1
β-strand	160-164	5	7
α-helix	165-168	4
β-strand	174-183	10	7
α-helix	184-189	6
β-strand	192-198	7	8
β-strand	206-211	6	8

Chains C and F: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	9
β-strand	14-15	2	10
β-strand	21-28	8	9
α-helix	32-34	3
β-strand	36-42	7	11
β-strand	49-55	7	11
β-strand	60-63	4	11
β-strand	71-76	6	9
β-strand	81-86	6	9
α-helix	91-93	3
β-strand	95-102	8	11
α-helix	106-109	4
β-strand	117	1	11
β-strand	121-123	3	11
β-strand	124-125	2	10
α-helix	128-130	3
β-strand	131	1	12
α-helix	132-133	2
β-strand	134-138	5	13
β-strand	150-159	10	13
β-strand	160	1	12
β-strand	165-168	4	14
α-helix	169-171	3
β-strand	173	1	14
β-strand	177-179	3	13
α-helix	180-182	3
β-strand	183-184	2	13
β-strand	190-198	9	13
α-helix	200-202	3
β-strand	209-214	6	14
α-helix	215-217	3
β-strand	219-224	6	14

Chain E: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	18
β-strand	11-14	4	19
β-strand	20-26	7	18
β-strand	34-39	6	19
β-strand	46-50	5	19
β-strand	54-55	2	19
α-helix	56	1
β-strand	63-68	6	18
β-strand	71-76	6	18
α-helix	81-83	3
β-strand	86-91	6	19
α-helix	97	1
β-strand	98-99	2	19
β-strand	103-107	5	19
β-strand	112	1	20
β-strand	115-119	5	21
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	21
β-strand	141	1	20
β-strand	146-151	6	22
β-strand	154-155	2	22
α-helix	156	1
β-strand	160-164	5	21
α-helix	165-168	4
β-strand	174-183	10	21
α-helix	184-189	6
β-strand	193-198	6	22
β-strand	206-210	5	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tudor and KH domain-containing protein	A, D	protein	222	Homo sapiens	Q9Y2W6 (AlphaFold model)
Uncharacterized protein	B, E	protein	226	Homo sapiens
Fab antigen-binding fragment	C, F	protein	244	Homo sapiens
Piwi-like protein 1	G	protein	16	Homo sapiens	Q96J94 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6PI7_1 Tudor and KH domain-containing protein (chains A, D)
GDEYLEVYVSASEHPNHFWIQIVGSRSLQLDKLVNEMTQHYENSVPEDLTVHVGDIVAAP
LPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLAR
IAPSGDQWEEEALDEFDRLTHCADWKPLVAKISSYVQTGISTWPKIYLYDTSNGKKLDIG
LELVHKGYAIELPEDIEENRAVPDMLKDMATETDASLSTLLT

Sequence of entity 2 (B, E), FASTA

>6PI7_2 Uncharacterized protein (chains B, E)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQAFWDPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECGGSDYKDDDDK

Sequence of entity 3 (C, F), FASTA

>6PI7_3 Fab antigen-binding fragment (chains C, F)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVSYYYIHWVRQAPGKGLEWVASIYPYYGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSHYRPWYKWAYGLDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTGGSHH
HHHH

Sequence of entity 4 (G), FASTA

>6PI7_4 Piwi-like protein 1 (chains G)
TGRARARARGRARGQE

Primary citation

Lesson from a Fab-enabled co-crystallization study of TDRD2 and PIWIL1. Chen, S., Zhang, W., Min, J. et al. Methods (2020) 175:72-78. DOI 10.1016/j.ymeth.2019.07.002 · PubMed

Other PDB entries of the same protein (UniProt Q9Y2W6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FDR 1.75 Å, Crystal structure of TDRD2
6B57 1.93 Å, tudor in complex with ligand
5J39 1.95 Å, Crystal Structure of the extended TUDOR domain from TDRD2
2DIQ Solution structure of the TUDOR domain of Tudor and KH domain containing protein

Browse structure collections

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