SMTL ID : 9vd9.1

Cryo-EM structure of the human DSS1-INTAC-PEC complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x THR- SER- PRO- SER- TYR- SER- PRO- THR: THR-SER-PRO-SER-TYR-SER-PRO-THR(Non-covalent)

THR-SER-PRO-SER-TYR-SER-PRO-THR.1: 6 residues within 4Å: Chain 6: N.543, Y.545, D.546 Chain E: E.925, K.1013, Q.1048 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain 6 Hydrogen bonds: E:N.928, E:K.1013, 6:N.543, 6:N.543

1 x SER- PRO- THR- SER: SER-PRO-THR-SER(Non-covalent)

SER-PRO-THR-SER.2: 5 residues within 4Å: Chain F: L.525, L.526, D.541, A.543, Y.544 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:L.525

1 x SER- PRO- LYS- TYR- SER- PRO- THR- SER: SER-PRO-LYS-TYR-SER-PRO-THR-SER(Non-covalent)

SER-PRO-LYS-TYR-SER-PRO-THR-SER.3: 8 residues within 4Å: Chain J: R.89, H.118, P.213, R.214, Y.265, C.266, R.268, C.269 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:Y.265 Hydrogen bonds: J:R.89, J:R.89, J:R.268

10 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain C: D.72, H.73, D.178, H.414 Chain D: U.1 Ligands: ZN.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.73, C:D.178, C:H.414 ZN.5: 7 residues within 4Å: Chain C: H.68, H.70, H.73, H.157, D.178 Chain D: U.1 Ligands: ZN.4 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.68, C:H.70, C:H.157, C:D.178 ZN.9: 5 residues within 4Å: Chain K: C.111, C.114, C.154, C.184, Q.188 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.111, K:C.114, K:C.154, K:C.184 ZN.10: 4 residues within 4Å: Chain K: C.71, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.71, K:C.74, K:C.81, K:H.84 ZN.11: 4 residues within 4Å: Chain L: C.1245, C.1248, C.1263, C.1266 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.1245, L:C.1248, L:C.1263, L:C.1266 ZN.12: 4 residues within 4Å: Chain M: C.88, C.90, C.94, C.97 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.88, M:C.90, M:C.94, M:C.97 ZN.13: 4 residues within 4Å: Chain Q: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.17, Q:C.20, Q:C.39, Q:C.42 ZN.14: 5 residues within 4Å: Chain Q: C.86, C.89, C.114, A.116, C.119 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.86, Q:C.89, Q:C.114, Q:C.119 ZN.15: 5 residues within 4Å: Chain R: C.7, T.9, C.10, C.44, C.45 5 PLIP interactions: 5 interactions with chain R Metal complexes: R:C.7, R:T.9, R:C.10, R:C.44, R:C.45 ZN.16: 5 residues within 4Å: Chain T: C.19, C.22, C.36, E.38, C.39 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.19, T:C.22, T:C.36, T:C.39

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.6: 4 residues within 4Å: Chain J: D.85, N.117, H.167, H.241 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:D.85, J:H.167, J:H.241 MN.7: 4 residues within 4Å: Chain J: D.57, H.59, D.85, H.118 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:H.59, J:D.85

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 5 residues within 4Å: Chain D: U.21 Chain K: R.460, D.495, D.497, D.499 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, C. et al., The small but versatile DSS1 protein is required for proper Integrator-PP2A function. To Be Published

Release Date

2025-06-25

Peptides

26S proteasome complex subunit SEM1: A
Integrator complex subunit 9: B
Integrator complex subunit 11: C
Integrator complex subunit 2: E
Integrator complex subunit 4: F
Integrator complex subunit 7: G
DNA-directed RNA polymerase II subunit RPB1: H
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform: I
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform: J
DNA-directed RNA polymerase II subunit RPB1: K
DNA-directed RNA polymerase subunit beta,DNA-directed RNA polymerase II subunit RPB2: L
DNA-directed RNA polymerase II subunit RPB3: M
DNA-directed RNA polymerases I, II, and III subunit RPABC1: N
DNA-directed RNA polymerases I, II, and III subunit RPABC2: O
DNA-directed RNA polymerases I, II, and III subunit RPABC3: P
DNA-directed RNA polymerase II subunit RPB9: Q
DNA-directed RNA polymerases I, II, and III subunit RPABC5: R
DNA-directed RNA polymerase II subunit RPB11-a: S
DNA-directed RNA polymerases I, II, and III subunit RPABC4: T
Negative elongation factor A: W
Negative elongation factor B: X
Negative elongation factor C/D: Y
Negative elongation factor E: Z
Transcription elongation factor SPT4: 0
Transcription elongation factor SPT5: 1
DNA-directed RNA polymerase II subunit RPB7: 2
DNA-directed RNA polymerase II subunit RPB4: 3
Integrator complex subunit 1: 4
Integrator complex subunit 5: 5
Integrator complex subunit 6: 6
Integrator complex subunit 8: 7
Unknown2: 8

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

B
I

C
K

E
B

F
D

G
G

H
m

I
P

J
Q

K
1

L
2

M
3

N
4

O
5

P
6

Q
7

R
8

S
9

T
a

W
e

X
f

Y
g

Z
h

0
i

1
j

2
k

3
l

4
A

5
E

6
F

7
H

8
M

26S proteasome complex subunit SEM1

Integrator complex subunit 9

Integrator complex subunit 11

Integrator complex subunit 2

Integrator complex subunit 4

Integrator complex subunit 7

DNA-directed RNA polymerase II subunit RPB1

Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform

Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase subunit beta,DNA-directed RNA polymerase II subunit RPB2

DNA-directed RNA polymerase II subunit RPB3

DNA-directed RNA polymerases I, II, and III subunit RPABC1

DNA-directed RNA polymerases I, II, and III subunit RPABC2

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase II subunit RPB9

DNA-directed RNA polymerases I, II, and III subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11-a

DNA-directed RNA polymerases I, II, and III subunit RPABC4

Negative elongation factor A

Negative elongation factor B

Negative elongation factor C/D

Negative elongation factor E

Transcription elongation factor SPT4

Transcription elongation factor SPT5

DNA-directed RNA polymerase II subunit RPB7

DNA-directed RNA polymerase II subunit RPB4

Integrator complex subunit 1

Integrator complex subunit 5

Integrator complex subunit 6

Integrator complex subunit 8

Unknown2

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