Uniprot accession / id : Q78PY7  OR   Uniprot accession / id : Q7KZF4
 
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Entry Information
Entry status  (1)
REL
(11)
 
Experimental methods  (2)
X-ray diffraction
(10)
Solution NMR
(1)
 
Authors  (79)
Arrowsmith CH
(3)
Bountra C
(3)
Edwards AM
(3)
Kang Y
(3)
Liu ZJ
(3)
Shen M
(3)
Silvennoinen O
(3)
Structural Genomics Consortium (SGC)
(3)
Wan L
(3)
Wang BC
(3)
Wei Y
(3)
Xing Y
(3)
Xu H
(3)
Yang J
(3)
Zhao M
(3)
Zheng A
(3)
Bertino J
(2)
Bian C
(2)
Bian CB
(2)
Bochkarev A
(2)
Chen C
(2)
Cheng C
(2)
Guo Y
(2)
Guo YH
(2)
Hang X
(2)
Jiang YZ
(2)
Jin J
(2)
Jin JF
(2)
Kim H
(2)
Lam R
(2)
Liu K
(2)
Lu X
(2)
MacKenzie F
(2)
Min J
(2)
Pawson T
(2)
Raba M
(2)
Remiszewski S
(2)
Rowicki M
(2)
Shao ZM
(2)
Smith HA
(2)
Southeast Collaboratory for Structural Genomics (SECSG)
(2)
Weigelt J
(2)
Wu CG
(2)
Wu S
(2)
Xu C
(2)
Yuan M
(2)
Zhang L
(2)
Zhao DY
(2)
Chan C
(1)
Chen YP
(1)
Dang W
(1)
Fedorov O
(1)
Guo F
(1)
Inoue M
(1)
Kigawa T
(1)
Knapp S
(1)
La Thangue NB
(1)
Lee W
(1)
Li CL
(1)
Moehlenbrink J
(1)
Muto Y
(1)
Nunez-Alonso G
(1)
RIKEN Structural Genomics/Proteomics Initiative (RSGI)
(1)
Rao Z
(1)
Satyshur K
(1)
Satyshur KA
(1)
Savitsky P
(1)
Shah N
(1)
Shaw N
(1)
Shirouzu M
(1)
Siejka P
(1)
Sorrell FJ
(1)
Stanevich V
(1)
Tallant C
(1)
Terada T
(1)
Yang WZ
(1)
Yokoyama S
(1)
Yuan HS
(1)
von Delft F
(1)
 
Homo / hetero assembly  (2)
homo
(6)
hetero
(5)
 
Assembly composition  (2)
protein structure
(6)
protein/protein complex
(5)
 
Assembly polymer count  (2)
dimer
(7)
monomer
(4)
 
Resolution distribution
1.0 - 1.5
(2)
1.5 - 2
(5)
2.5 - 3
(3)
 
Release year distribution
2005 - 2010
(7)
2010 - 2015
(3)
2015 - 2020
(1)
2020 - 2025
(2)
 
Journal  (5)
To be published
(5)
Nat Cancer
(2)
Proc Natl Acad Sci U S A
(2)
Cell Rep
(1)
Nucleic Acids Res
(1)
 
Macromolecules
Organism superkingdom  (1)
Eukaryota
(11)
 
Organism name  (1)
Homo sapiens
(11)
 
Molecule name  (5)
100 kDa coactivator
(11)
EBNA2 coactivator p100
(11)
Staphylococcal nuclease domain-containing protein 1
(11)
Tudor domain-containing protein 11
(11)
p100 co-activator
(11)
 
Molecule type  (1)
Protein
(11)
 
Gene names  (2)
SND1
(11)
TDRD11
(11)
 
Interacting Molecules  (5)
Protein LYRIC
(1)
SYNTHETIC PEPTIDE
(1)
Staphylococcal nuclease domain-containing protein 1
(1)
Transcription factor E2F1
(1)
dimethylated arginine peptide R14me2s
(1)
 
Interacting ligands  (8)
GOL : GLYCEROL
(3)
CIT : CITRIC ACID
(1)
CL : CHLORIDE ION
(1)
CS : CESIUM ION
(1)
QOV : 5-chloro-2-methoxy-N-(2-methyl[1,2,4]triazolo[1,5-a]pyridin-8-yl)benzene-1-sulfonamide
(1)
QOY : 5-chloro-2-methoxy-N-([1,2,4]triazolo[1,5-a]pyridin-8-yl)benzene-1-sulfonamide
(1)
SO4 : SULFATE ION
(1)
TYR : TYROSINE
(1)
 
Function and Biology
EC number / name  (1)
3.1.31.1 : Micrococcal nuclease
(11)
 
Biological function  (2)
nuclease activity
(3)
nucleic acid binding
(3)
 
Sequence and Structure classification
SCOP fold  (1)
SH3-like barrel
(1)
 
SCOP family  (1)
Tudor domain
(1)
 
CATH class  (1)
Mainly Beta
(9)
 
CATH topology  (2)
SH3 type barrels.
(8)
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(7)
 
Pfam accession / name  (2)
PF00565 : SNase
(10)
PF00567 : TUDOR
(8)
 
Experimental Information
Diffraction protocol  (2)
Single wavelength
(9)
MAD
(1)
 
Diffraction radiation source type  (3)
Synchrotron
(6)
Liquid anode
(2)
Rotating anode
(2)
 
Diffraction source  (6)
APS BEAMLINE 22-ID
(3)
BRUKER METALJET
(2)
RIGAKU FR-E SUPERBRIGHT
(2)
APS BEAMLINE 21-ID-D
(1)
DIAMOND BEAMLINE I04
(1)
SPRING-8 BEAMLINE BL12B2
(1)
 
Synchrotron site  (3)
APS
(4)
Diamond
(1)
SPring-8
(1)
 
Diffraction detector type  (3)
CCD
(6)
Pixel
(3)
Image plate
(1)
 
Refinement software  (3)
REFMAC
(8)
CNS
(1)
PHENIX
(1)
 
NMR
NMR software packages  (5)
CYANA
(1)
KUJIRA
(1)
NMRPipe
(1)
NMRView
(1)
XwinNMR
(1)
 
NMR Field Strength
700.0 - 800
(1)
800.0 - 900
(1)
 
Representative Structures
Representative Structures
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Entries 1 to 10 of 11
Entries 1 to 10 of 11
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Crystal structure of human SND1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide
Tallant C, Savitsky P, Moehlenbrink J, Chan C, Nunez-Alonso G, Siejka P, Sorrell FJ, von Delft F, Arrowsmith CH, Edwards AM, Bountra C, Fedorov O, La Thangue NB, Knapp S, Structural Genomics Consortium (SGC)
To be published
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Modified residues: 2MR    2MR   
Assembly name: Transcription factor E2F1 and Staphylococcal nuclease domain-containing protein 1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-169517 (Preferred)   search this ID
PDBe-KB: Q7KZF4    Q01094   
X-ray diffraction
1.45Å resolution
Released: 7 Dec 2016
Model geometry
Fit model/data
5m9o
5m9o
5m9o
Crystal structure of SND1 in complex with C-26-A6
Kang Y
Nat Cancer (2022) [PMID: 35121987  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: QOV    GOL    QOV    TYR    TYR   
Assembly name: Staphylococcal nuclease domain-containing protein 1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-181614 (Preferred)   search this ID
PDBe-KB: Q7KZF4   
X-ray diffraction
2.7Å resolution
Released: 8 Dec 2021
Model geometry
Fit model/data
7knx
7knx
7knx
Crystal structure of SND1 in complex with C-26-A2
Kang Y
Nat Cancer (2022) [PMID: 35121987  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: GOL    QOY    QOY   
Assembly name: Staphylococcal nuclease domain-containing protein 1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-181614 (Preferred)   search this ID
PDBe-KB: Q7KZF4   
X-ray diffraction
2.65Å resolution
Released: 8 Dec 2021
Model geometry
Fit model/data
7knw
7knw
7knw
Crystal structure of a truncated human Tudor-SN
Li CL
Nucleic Acids Res (2008) [PMID: 18453631  ]
Source organism: Homo sapiens  
Assembly composition: protein only structure
Bound ligands: CIT   
Assembly name: Staphylococcal nuclease domain-containing protein 1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-181614 (Preferred)   search this ID
PDBe-KB: Q7KZF4   
X-ray diffraction
1.9Å resolution
Released: 26 Aug 2008
Model geometry
Fit model/data
3bdl
3bdl
3bdl
Crystal structure of human P100 Tudor domain: Large fragment
Shah N, Zhao M, Cheng C, Xu H, Yang J, Silvennoinen O, Liu ZJ, Wang BC, Southeast Collaboratory for Structural Genomics (SECSG)
To be published
Source organism: Homo sapiens  
Assembly composition: protein only structure
Assembly name: Staphylococcal nuclease domain-containing protein 1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-181617 (Preferred)   search this ID
PDBe-KB: Q7KZF4   
X-ray diffraction
2Å resolution
Released: 3 Jul 2007
Model geometry
Fit model/data
2hqe
2hqe
2hqe
Crystal structure of human P100 tudor domain
Shaw N, Zhao M, Cheng C, Xu H, Yang J, Silvennoinen O, Rao Z, Wang BC, Liu ZJ
To be published
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Assembly name: Staphylococcal nuclease domain-containing protein 1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-181615 (Preferred)   search this ID
PDBe-KB: Q7KZF4   
X-ray diffraction
2Å resolution
Released: 13 Feb 2007
Model geometry
Fit model/data
Data not deposited
2o4x
2o4x
2o4x
Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R14me2s
Lam R, Liu K, Guo YH, Bian CB, Xu C, MacKenzie F, Bountra C, Weigelt J, Arrowsmith CH, Edwards AM, Bochkarev A, Min J, Structural Genomics Consortium (SGC)
Proc Natl Acad Sci U S A (2010) [PMID: 20937909  ]
Source organisms: Synthetic construct, Homo sapiens  
Assembly composition: protein/protein complex
Modified residues: 2MR    2MR   
Assembly name: Staphylococcal nuclease domain-containing protein 1 and peptide (Preferred)   search this complex
PDBe complex ID: PDB-CPX-163864 (Preferred)   search this ID
PDBe-KB: Q7KZF4   
X-ray diffraction
1.85Å resolution
Released: 8 Sep 2010
Model geometry
Fit model/data
3omg
3omg
3omg
Solution structure of the TUDOR domain of Staphylococcal nuclease domain-containing protein 1
Dang W, Muto Y, Inoue M, Kigawa T, Shirouzu M, Terada T, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
To be published
Source organism: Homo sapiens  
Assembly composition: protein only structure
Assembly name: Staphylococcal nuclease domain-containing protein 1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-181614 (Preferred)   search this ID
PDBe-KB: Q7KZF4   
Solution NMR
Released: 3 Jul 2007
Model geometry
Fit model/data
Data not analysed
2e6n
2e6n
2e6n
The Structure of MTDH-SND1 Complex Reveals Novel Cancer-Promoting Interactions
Guo F, Stanevich V, Wan L, Satyshur K, Kang Y, Xing Y
Cell Rep (2014) [PMID: 25242325  ]
Source organism: Homo sapiens  
Assembly composition: protein/protein complex
Bound ligands: CS    GOL    SO4    CS   
Modified residues: MSE    MSE   
Assembly name: Protein LYRIC and Staphylococcal nuclease domain-containing protein 1 (Preferred)   search this complex
PDBe complex ID: PDB-CPX-181616 (Preferred)   search this ID
PDBe-KB: Q7KZF4    Q86UE4   
X-ray diffraction
2.701Å resolution
Released: 8 Oct 2014
Model geometry
Fit model/data
4qmg
4qmg
4qmg
Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R4me2s
Lam R, Liu K, Guo YH, Bian CB, Xu C, MacKenzie F, Bountra C, Weigelt J, Arrowsmith CH, Edwards AM, Bochkarev A, Min J, Structural Genomics Consortium (SGC)
Proc Natl Acad Sci U S A (2010) [PMID: 20937909  ]
Assembly composition: protein/protein complex
Bound ligands: CL   
Modified residues: 2MR    2MR   
Assembly name: Staphylococcal nuclease domain-containing protein 1 and peptide (Preferred)   search this complex
PDBe complex ID: PDB-CPX-163862 (Preferred)   search this ID
PDBe-KB: Q7KZF4   
X-ray diffraction
1.77Å resolution
Released: 15 Sep 2010
Model geometry
Fit model/data
3omc
3omc
3omc
Entries 1 to 10 of 11
Entries 1 to 10 of 11