7L9P: Human SHLD2-SHLD3-REV7-TRIP13(E253Q) complex

Structure of human SHLD2-SHLD3-REV7-TRIP13(E253Q) complex. Determined by electron microscopy at 3.6 Å resolution. Released 3 Mar 2021.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 12
Atoms: 21,908
Mol. weight: 412.64 kDa
Ligands: AGS
Released: 3 Mar 2021

Explore 7L9P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7L9P contains 115 α-helices and 122 β-strands across 12 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: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	123-125	3	1
α-helix	145-162	18
β-strand	174-178	5	1
α-helix	185-199	15
β-strand	207-211	5	1
α-helix	215-217	3
α-helix	222-241	20
β-strand	246-253	8	1
α-helix	255-262	8
α-helix	270-287	18
β-strand	293-298	6	1
β-strand	315-318	4	1
α-helix	324-340	17
β-strand	344	1	2
α-helix	353-359	7
α-helix	369-379	11
α-helix	387-395	9
α-helix	396-400	5
β-strand	405	1	2
α-helix	407-427	21

Chain B: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	21-27	7	3
α-helix	35-49	15
β-strand	57-58	2	3
α-helix	64-69	6
β-strand	70-76	7	3
β-strand	95-100	6	3
β-strand	103	1	4
β-strand	108-110	3	5
β-strand	122-124	3	5
β-strand	129	1	4
α-helix	130-132	3
α-helix	135-138	4
α-helix	146-161	16
β-strand	175-178	4	6
α-helix	185-199	15
α-helix	200-202	3
β-strand	210-211	2	6
β-strand	212	1	5
α-helix	214-216	3
α-helix	224-240	17
β-strand	248-251	4	6
α-helix	254-256	3
α-helix	263-265	3
α-helix	271-273	3
α-helix	277-287	11
β-strand	294-299	6	6
β-strand	316-318	3	6
α-helix	324-340	17
β-strand	344	1	7
α-helix	353-358	6
α-helix	368-379	12
α-helix	387-400	14
β-strand	405	1	7
α-helix	407-427	21

Chain C: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	8
β-strand	22-27	6	9
α-helix	35-49	15
β-strand	57-59	3	9
α-helix	64-69	6
β-strand	70-76	7	9
β-strand	94	1	8
α-helix	95-97	3
β-strand	98-100	3	9
β-strand	103	1	10
β-strand	122-125	4	11
β-strand	129	1	10
α-helix	135-138	4
α-helix	145-161	17
β-strand	175-178	4	11
α-helix	192-199	8
β-strand	207	1	12
β-strand	209-212	4	11
α-helix	214-217	4
α-helix	229-240	12
β-strand	246	1	12
β-strand	248-251	4	11
α-helix	254-256	3
β-strand	259	1	13
α-helix	272-275	4
α-helix	277-280	4
β-strand	294-298	5	11
α-helix	302-304	3
β-strand	305	1	13
β-strand	317-318	2	11
α-helix	324-341	18
β-strand	344	1	14
α-helix	353-359	7
α-helix	367-379	13
α-helix	385-397	13
β-strand	405	1	14
α-helix	407-426	20

Chain D: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	21-27	7	15
α-helix	36-49	14
β-strand	56-58	3	15
α-helix	64-69	6
β-strand	72-76	5	15
β-strand	95-101	7	15
β-strand	110	1	16
β-strand	121	1	16
β-strand	123-125	3	17
α-helix	135-138	4
α-helix	144-160	17
β-strand	174-179	6	17
α-helix	187-199	13
β-strand	206-212	7	17
β-strand	221	1	18
α-helix	226-240	15
β-strand	245-251	7	17
α-helix	254-256	3
α-helix	272-286	15
β-strand	293-300	8	17
α-helix	307-310	4
β-strand	315-318	4	17
α-helix	324-341	18
α-helix	353-358	6
α-helix	365-379	15
α-helix	385-388	4
α-helix	391-394	4
α-helix	411-427	17

Chain E: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	21-26	6	19
α-helix	35-49	15
β-strand	57-58	2	19
α-helix	64-69	6
β-strand	72-76	5	19
β-strand	95-100	6	19
β-strand	103	1	20
β-strand	108-110	3	21
β-strand	122-127	6	21
β-strand	129	1	20
α-helix	130-132	3
α-helix	135-138	4
α-helix	145-161	17
β-strand	174-178	5	21
α-helix	187-199	13
β-strand	207-212	6	21
α-helix	225-240	16
β-strand	246-252	7	21
α-helix	254-257	4
α-helix	272-275	4
α-helix	283-287	5
β-strand	293-299	7	21
β-strand	315-318	4	21
α-helix	320-322	3
α-helix	324-340	17
β-strand	344	1	22
α-helix	349-352	4
α-helix	353-359	7
α-helix	368-379	12
α-helix	385-395	11
β-strand	405	1	22
α-helix	410-427	18

Chain F: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	123	1	23
β-strand	126	1	23
α-helix	136-138	3
α-helix	148-161	14
β-strand	174-178	5	23
α-helix	185-198	14
β-strand	206-212	7	23
α-helix	231-238	8
β-strand	245-252	8	23
α-helix	281-287	7
β-strand	293-298	6	23
α-helix	307-310	4
β-strand	315-318	4	23
α-helix	322-323	2
α-helix	324-340	17
β-strand	344	1	24
α-helix	353-359	7
α-helix	369-375	7
α-helix	380-382	3
α-helix	385-395	11
α-helix	396-400	5
β-strand	405	1	24
α-helix	407-423	17

Chain G: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	16-33	18
α-helix	39-41	3
β-strand	43-47	5	25
β-strand	50-54	5	25
α-helix	58-77	20
β-strand	80-87	8	26
β-strand	96-103	8	26
α-helix	119-131	13
β-strand	146-152	7	26
α-helix	157-163	7
α-helix	170	1
β-strand	171-173	3	27
β-strand	190-193	4	26
β-strand	198-205	8	26

Chain I: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	18
α-helix	15-33	19
β-strand	42-44	3	28
β-strand	47	1	29
β-strand	50	1	29
β-strand	53-55	3	28
α-helix	58-67	10
β-strand	82-88	7	30
β-strand	94-102	9	30
α-helix	118-133	16
α-helix	140-141	2
β-strand	145-151	7	30
α-helix	160-163	4
β-strand	171-172	2	31
β-strand	185-187	3	30
β-strand	193	1	32
β-strand	198	1	32
β-strand	199-205	7	30

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pachytene checkpoint protein 2 homolog	A, B, C, D, E, F	protein	432	Homo sapiens	Q15645 (AlphaFold model)
Mitotic spindle assembly checkpoint protein MAD2B	G, I, J, K	protein	211	Homo sapiens	Q9UI95 (AlphaFold model)
Shieldin complex subunit 2, Shieldin complex subunit 3 chimera	X, Y	protein	99	Homo sapiens	Q6ZNX1 (AlphaFold model), Q86V20 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>7L9P_1 Pachytene checkpoint protein 2 homolog (chains A, B, C, D, E, F)
SDEAVGDLKQALPCVAESPTVHVEVHQRGSSTAKKEDINLSVRKLLNRHNIVFGDYTWTE
FDEPFLTRNVQSVSIIDTELKVKDSQPIDLSACTVALHIFQLNEDGPSSENLEEETENII
AANHWVLPAAEFHGLWDSLVYDVEVKSHLLDYVMTTLLFSDKNVNSNLITWNRVVLLHGP
PGTGKTSLCKALAQKLTIRLSSRYRYGQLIEINSHSLFSKWFSESGKLVTKMFQKIQDLI
DDKDALVFVLIDQVESLTAARNACRAGTEPSDAIRVVNAVLTQIDQIKRHSNVVILTTSN
ITEKIDVAFVDRADIKQYIGPPSAAAIFKIYLSCLEELMKCQIIYPRQQLLTLRELEMIG
FIENNVSKLSLLLNDISRKSEGLSGRVLRKLPFLAHALYVQAPTVTIEGFLQALSLAVDK
QFEERKKLAAYI

Sequence of entity 2 (G, I, J, K), FASTA

>7L9P_2 Mitotic spindle assembly checkpoint protein MAD2B (chains G, I, J, K)
STTLTRQDLNFGQVVADVLCEFLEVAVHLILYVREVYPVGIFQKRKKYNVPVQMSCHPEL
NQYIQDTLHCVKPLLEKNDVEKVVVVILDKEHRPVEKFVFEITQPPLLSISSDSLLSHVE
QLLRAFILKISVCDAVLDHNPPGCTFTVLVHTREAATRNMEKIQVIKDFPWILADEQDVH
MHDPRLIPLKTMTSDILKMQLYVEERAHKGS

Sequence of entity 3 (X, Y), FASTA

>7L9P_3 Shieldin complex subunit 2, Shieldin complex subunit 3 chimera (chains X, Y)
MSQVHIFWGAPIAPLKGSGSGSGSGSGSGSGSTTEVILHYRPCESDPTQLPKIAEKAIQD
FPTRPLSRFIPWFPYDGSKLPLRPKRSPPASREEIMATL

Ligands and cofactors

ID	Name	Formula	Copies
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	5

Primary citation

Molecular mechanisms of assembly and TRIP13-mediated remodeling of the human Shieldin complex. Xie, W., Wang, S., Wang, J. et al. Proc Natl Acad Sci U S A (2021) 118. DOI 10.1073/pnas.2024512118 · PubMed

Other PDB entries of the same protein (UniProt Q15645 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WC2 2.5 Å, Crystal Structure of ADP-bound human TRIP13
5VQA 2.54 Å, Structure of human TRIP13, ATP-bound form
6LK0 2.6 Å, Crystal structure of human wild type TRIP13
5VQ9 3.02 Å, Structure of human TRIP13, Apo form
6F0X 4.6 Å, Cryo-EM structure of TRIP13 in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20

Browse structure collections

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