3ASK - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF UHRF1 IN COMPLEX WITH HISTONE TAIL

Authors :   K. Arita, K. Sugita, M. Unoki, R. Hamamoto, N. Sekiyama, H. Tochio, M. Ar M. Shirakawa

Date :   16 Dec 10 (Deposition) - 25 Jan 12 (Release) - 05 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B,C,D,P,Q,R
Biol. Unit 1: A,P  (1x)
Biol. Unit 2: B,Q  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D,R  (1x)

Keywords :   Histone Reader Modules, Epigenetic Regulation, Histone H3, Trimethylaion Of Lysine Residue, Ligase-Dna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Arita, S. Isogai, T. Oda, M. Unoki, K. Sugita, N. Sekiyama, K. Kuwata R. Hamamoto, H. Tochio, M. Sato, M. Ariyoshi, M. Shirakawa
Recognition Of Modification Status On A Histone H3 Tail By Linked Histone Reader Modules Of The Epigenetic Regulator Uhrf1
Proc. Natl. Acad. Sci. Usa V. 109 12950 2012
PubMed-ID: 22837395 | Reference-DOI: 10.1073/PNAS.1203701109

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE UHRF1
	Chains	:	A, B, C, D
	EC Number	:	6.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	TANDEM TUDOR DOMAIN, PHD FINGER (RESIDUES 134-366)
	Gene	:	UHRF1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - HISTONE H3.3
	Chains	:	P, Q, R
	Engineered	:	YES
	Fragment	:	RESIDUES IN UNP 2-14
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2	3	4	5	6	7
Asymmetric Unit	:	A	B	C	D	P	Q	R
Biological Unit 1 (1x)	:	A				P
Biological Unit 2 (1x)	:		B				Q
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D			R

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	M3L	3	Mod. Amino Acid	N-TRIMETHYLLYSINE
2	ZN	7	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	M3L	-1	Mod. Amino Acid	N-TRIMETHYLLYSINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	M3L	1	Mod. Amino Acid	N-TRIMETHYLLYSINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:302 , CYS A:305 , CYS A:313 , CYS A:316 , ARG A:324	BINDING SITE FOR RESIDUE ZN A 501
2	AC2	SOFTWARE	CYS A:318 , CYS A:321 , HIS A:341 , CYS A:344	BINDING SITE FOR RESIDUE ZN A 502
3	AC3	SOFTWARE	CYS A:333 , CYS A:336 , CYS A:360 , CYS A:363	BINDING SITE FOR RESIDUE ZN A 503
4	AC4	SOFTWARE	CYS B:302 , CYS B:305 , CYS B:313 , CYS B:316	BINDING SITE FOR RESIDUE ZN B 504
5	AC5	SOFTWARE	CYS B:318 , CYS B:321 , HIS B:341 , CYS B:344	BINDING SITE FOR RESIDUE ZN B 505
6	AC6	SOFTWARE	CYS B:333 , CYS B:336 , CYS B:360 , CYS B:363	BINDING SITE FOR RESIDUE ZN B 506
7	AC7	SOFTWARE	CYS C:302	BINDING SITE FOR RESIDUE ZN C 501

(no "SS Bond" information available for 3ASK)

Asymmetric Unit

No.	Residues
1	Gly A:299	-	Pro A:300
2	Gly B:299	-	Pro B:300

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022554	D	240	H	UHRF1_HUMAN	Polymorphism	17886098	A/B/C/D	D	240	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022554	D	240	H	UHRF1_HUMAN	Polymorphism	17886098	A	D	240	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022554	D	240	H	UHRF1_HUMAN	Polymorphism	17886098	B	D	240	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022554	D	240	H	UHRF1_HUMAN	Polymorphism	17886098	C	D	240	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_022554	D	240	H	UHRF1_HUMAN	Polymorphism	17886098	D	D	240	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (3, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	3	A:302-363 B:302-363 C:302-302
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	2	A:310-364 B:310-363
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	2	A:318-364 B:318-363 -

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	1	A:302-363 - -
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	1	A:310-364 -
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	1	A:318-364 - -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	1	- B:302-363 -
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	1	- B:310-363
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	1	- B:318-363 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	1	- - C:302-302
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	0	- -
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	0	- - -

Biological Unit 4 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_1	PS01359	Zinc finger PHD-type signature.	UHRF1_HUMAN	302-363	0	- - -
2	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	UHRF1_HUMAN	310-366	0	- -
3	ZF_RING_2	PS50089	Zinc finger RING-type profile.	UHRF1_HUMAN	318-364 724-763	0	- - -

Asymmetric Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000366816	1	ENSE00001442675	chr1:226249552-226249795	244	H33_HUMAN	-	0	0	-	-
1.2c	ENST00000366816	2c	ENSE00001442674	chr1:226250436-226250512	77	H33_HUMAN	-	0	0	-	-
1.3b	ENST00000366816	3b	ENSE00001428176	chr1:226252030-226252180	151	H33_HUMAN	1-43	43	2	P:1-10 Q:1-9 -	10 9 -
1.4a	ENST00000366816	4a	ENSE00001692850	chr1:226253357-226253510	154	H33_HUMAN	43-94	52	0	-	-
1.5a	ENST00000366816	5a	ENSE00001381318	chr1:226259052-226259224	173	H33_HUMAN	95-136	42	0	-	-

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:213
 aligned with UHRF1_HUMAN | Q96T88 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:232
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362  
          UHRF1_HUMAN   133 GLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPECR 364
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee......eeeeeeeeeee..---------------...eeeeeee..hhhh.eeeee...eee......hhhhh....eeeeee.........eeeeeeeeeeee....eeeeeeee....eeeeeee......................................................--...ee......ee....--.............hhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------H---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZF_PHD_1  PDB: A:302-363 UniProt: 302-363                     - PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZF_PHD_2  PDB: A:310-364 UniProt: 310-366               PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZF_RING_2  PDB: A:318-364 UniProt: 318-364      PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ask A 133 SLYKVNEYVDARDTNMGAWFEAQVVRVTRKA---------------EEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGPSCKHCKDDVNRLCRVCACHLCGGRQ--DKQLMCDECDMAFHIYC--PPLSSVPSEDEWYCPECR 364
                                   142       152       162|        -      |182       192       202       212       222       232       242       252       262       272       282       292       302       312       322  |  | 332       342 |  |  352       362  
                                                        163             179                                                                                                                                               325  |             344  |                 
                                                                                                                                                                                                                             328                347

Chain B from PDB  Type:PROTEIN  Length:211
 aligned with UHRF1_HUMAN | Q96T88 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:231
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362 
          UHRF1_HUMAN   133 GLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYCPEC 363
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee......eeeeeeeeeee.-----------------..eeeeeee..hhhh.eeeee...eee......hhhhh....eeeeee.........eeeeeeeeeeee....eeeeeeee....eeeeeee......................................................hhh.eee......eee...---................ Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------H--------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZF_PHD_1  PDB: B:302-363 UniProt: 302-363                      PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZF_PHD_2  PDB: B:310-363 UniProt: 310-366              PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZF_RING_2  PDB: B:318-363 UniProt: 318-364     PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ask B 133 SLYKVNEYVDARDTNMGAWFEAQVVRVTRK-----------------EDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGPSCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYC---PLSSVPSEDEWYCPEC 363
                                   142       152       162         -       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342 |   | 352       362 
                                                       162               180                                                                                                                                                                 344 348

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with UHRF1_HUMAN | Q96T88 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:170
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302
          UHRF1_HUMAN   133 GLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGPSC 302
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee......eeeeeeeeeee.----------------...eeeeeee..hhhh.eeeee...eee......hhhhh....eeeeee.........eeeeeeeeeeee....eeeeeeee....eeeeeee............................... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------H-------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------Z PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ask C 133 SLYKVNEYVDARDTNMGAWFEAQVVRVTRK----------------EEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGPSC 302
                                   142       152       162         -      |182       192       202       212       222       232       242       252       262       272       282       292       302
                                                       162              179

Chain D from PDB  Type:PROTEIN  Length:152
 aligned with UHRF1_HUMAN | Q96T88 from UniProtKB/Swiss-Prot  Length:793

    Alignment length:169
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292         
          UHRF1_HUMAN   133 GLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGPS 301
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee......eeeeeeeeee.-----------------....eeeeee..hhhh.eeeee...eee......hhhhh....eeeeee.........eeeeeeeeeeee....eeeeeeee....eeeeeee.............................. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------H------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ask D 133 SLYKVNEYVDARDTNMGAWFEAQVVRVTR-----------------EEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGPS 301
                                   142       152        |-         -      |182       192       202       212       222       232       242       252       262       272       282       292         
                                                      161               179

Chain P from PDB  Type:PROTEIN  Length:10
 aligned with H33_HUMAN | P84243 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:10
                                    11
            H33_HUMAN     2 ARTKQTARKS  11
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
           Transcript 1 (1) Exon 1.3b  Transcript 1 (1)
           Transcript 1 (2) ---------- Transcript 1 (2)
                 3ask P   1 ARTKQTARkS  10
                                    10
                                    9-M3L

Chain Q from PDB  Type:PROTEIN  Length:9
 aligned with H33_HUMAN | P84243 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:9
            H33_HUMAN     2 ARTKQTARK  10
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
           Transcript 1 (1) Exon 1.3b Transcript 1 (1)
           Transcript 1 (2) --------- Transcript 1 (2)
                 3ask Q   1 ARTKQTARk   9
                                    |
                                    9-M3L

Chain R from PDB  Type:PROTEIN  Length:1
 aligned with H33_HUMAN | P84243 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:1
            H33_HUMAN     2 K 123
               SCOP domains - SCOP domains
               CATH domains - CATH domains
               Pfam domains - Pfam domains
         Sec.struct. author . Sec.struct. author
                 SAPs(SNPs) - SAPs(SNPs)
                    PROSITE - PROSITE
           Transcript 1 (1) 1 Transcript 1 (1)
           Transcript 1 (2) - Transcript 1 (2)
                 3ask R   1 k   9
                                     |
                                     |
                                     9-M3L

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3ASK)

(no "CATH Domain" information available for 3ASK)

(no "Pfam Domain" information available for 3ASK)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (UHRF1_HUMAN | Q96T88)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000987	core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.
	GO:0044729	hemi-methylated DNA-binding	Interacting selectively and non-covalently with double-stranded hemi-methylated DNA at replication foci (one strand methylated, while the other strand is unmethylated). Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks.
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008327	methyl-CpG binding	Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
	GO:0035064	methylated histone binding	Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
	GO:0031493	nucleosomal histone binding	Interacting selectively and non-covalently with a histone that is assembled into a nucleosome.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0061630	ubiquitin protein ligase activity	Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0010390	histone monoubiquitination	The modification of histones by addition of a single ubiquitin group.
	GO:0016574	histone ubiquitination	The modification of histones by addition of ubiquitin groups.
	GO:0010216	maintenance of DNA methylation	Any process involved in maintaining the methylation state of a nucleotide sequence.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:2000373	positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity	Any process that activates or increases the frequency, rate or extent of DNA topoisomerase (ATP-hydrolyzing) activity.
	GO:0032270	positive regulation of cellular protein metabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0051865	protein autoubiquitination	The ubiquitination by a protein of one or more of its own amino acid residues, or residues on an identical protein. Ubiquitination occurs on the lysine residue by formation of an isopeptide crosslink.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0042787	protein ubiquitination involved in ubiquitin-dependent protein catabolic process	The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
	GO:0090308	regulation of methylation-dependent chromatin silencing	Any process that modulates the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000791	euchromatin	A dispersed and relatively uncompacted form of chromatin.
	GO:0000792	heterochromatin	A compact and highly condensed form of chromatin.
	GO:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	GO:0005720	nuclear heterochromatin	A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
	GO:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005657	replication fork	The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.

Chain P,Q,R (H33_HUMAN | P84243)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000979	RNA polymerase II core promoter sequence-specific DNA binding	Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
	GO:0000980	RNA polymerase II distal enhancer sequence-specific DNA binding	Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
	GO:0031492	nucleosomal DNA binding	Interacting selectively and non-covalently with the DNA portion of a nucleosome.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0006336	DNA replication-independent nucleosome assembly	The formation of nucleosomes outside the context of DNA replication.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0007420	brain development	The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0000183	chromatin silencing at rDNA	Repression of transcription of ribosomal DNA by altering the structure of chromatin.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0045814	negative regulation of gene expression, epigenetic	Any epigenetic process that stops, prevents or reduces the rate of gene expression.
	GO:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0030307	positive regulation of cell growth	Any process that activates or increases the frequency, rate, extent or direction of cell growth.
	GO:0045815	positive regulation of gene expression, epigenetic	Any epigenetic process that activates or increases the rate of gene expression.
	GO:0009725	response to hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
	GO:0032200	telomere organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0000228	nuclear chromosome	A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0000788	nuclear nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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	UHRF1_HUMAN \| Q96T88
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2faz	UBIQUITIN-LIKE DOMAIN OF HUMAN NUCLEAR ZINC FINGER PROTEIN NP95
2zkd	CRYSTAL STRUCTURE OF THE SRA DOMAIN OF MOUSE NP95 IN COMPLEX WITH HEMI-METHYLATED CPG DNA
2zo0	MOUSE NP95 SRA DOMAIN DNA SPECIFIC COMPLEX 1
3asl
3clz	THE SET AND RING ASSOCIATED (SRA) DOMAIN OF UHRF1 BOUND TO METHYLATED DNA
3db3	CRYSTAL STRUCTURE OF THE TANDEM TUDOR DOMAINS OF THE E3 UBIQUITIN-PROTEIN LIGASE UHRF1 IN COMPLEX WITH TRIMETHYLATED HISTONE H3-K9 PEPTIDE
3fl2	CRYSTAL STRUCTURE OF THE RING DOMAIN OF THE E3 UBIQUITIN- PROTEIN LIGASE UHRF1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 4)

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Exons (1, 2)

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Gene Ontology (64, 68)

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