2PVC - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   DNMT3L RECOGNIZES UNMETHYLATED HISTONE H3 LYSINE 4

Authors :   X. Cheng

Date :   09 May 07 (Deposition) - 14 Aug 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.69

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: B,D  (1x)
Biol. Unit 2: A,E  (1x)
Biol. Unit 3: C,F  (1x)

Keywords :   Dnmt3L, Unmethylated H3K4, De Novo Dna Methylation, Transferase Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. K. Ooi, C. Qiu, E. Bernstein, K. Li, D. Jia, Z. Yang, H. Erdjument-Bromage, P. Tempst, S. P. Lin, C. D. Allis, X. Cheng, T. H. Bestor
Dnmt3L Connects Unmethylated Lysine 4 Of Histone H3 To De Novo Methylation Of Dna.
Nature V. 448 714 2007
PubMed-ID: 17687327 | Reference-DOI: 10.1038/NATURE05987
(for further references see the PDB file header)

Molecule 1 - DNA (CYTOSINE-5)-METHYLTRANSFERASE 3-LIKE
	Chains	:	B, A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET-28A,PXC391
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	DNMT3L
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - HISTONE H3 PEPTIDE
	Chains	:	D, E, F
	Engineered	:	YES
	Other Details	:	SYNTHETIC HISTONE H3 PEPTIDE
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:		B		D
Biological Unit 2 (1x)	:	A				E
Biological Unit 3 (1x)	:			C			F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 9)

No.	Name	Count	Type	Full Name
1	ZN	9	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:96 , ILE A:98 , CYS A:99 , CYS A:118 , CYS A:121	BINDING SITE FOR RESIDUE ZN A 602
2	AC2	SOFTWARE	CYS A:108 , CYS A:113 , CYS A:142 , CYS A:145	BINDING SITE FOR RESIDUE ZN A 603
3	AC3	SOFTWARE	CYS A:53 , CYS A:56 , CYS A:73 , CYS A:76	BINDING SITE FOR RESIDUE ZN A 601
4	AC4	SOFTWARE	CYS B:96 , CYS B:99 , CYS B:118 , CYS B:121	BINDING SITE FOR RESIDUE ZN B 605
5	AC5	SOFTWARE	CYS B:108 , CYS B:113 , CYS B:142 , CYS B:145	BINDING SITE FOR RESIDUE ZN B 606
6	AC6	SOFTWARE	CYS B:53 , CYS B:56 , CYS B:73 , CYS B:76	BINDING SITE FOR RESIDUE ZN B 604
7	AC7	SOFTWARE	CYS C:96 , CYS C:99 , CYS C:118 , CYS C:121	BINDING SITE FOR RESIDUE ZN C 608
8	AC8	SOFTWARE	CYS C:108 , CYS C:113 , CYS C:142 , CYS C:145	BINDING SITE FOR RESIDUE ZN C 609
9	AC9	SOFTWARE	CYS C:53 , CYS C:56 , CYS C:73 , CYS C:76	BINDING SITE FOR RESIDUE ZN C 607

Asymmetric Unit

No.	Residues
1	A:56	-	A:76
2	A:99	-	A:118
3	C:99	-	C:118

(no "Cis Peptide Bond" information available for 2PVC)

Asymmetric Unit (1, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051962	R	278	G	DNM3L_HUMAN	Polymorphism	7354779	A/B/C	G	278	G

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_051962	R	278	G	DNM3L_HUMAN	Polymorphism	7354779	B	G	278	G

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_051962	R	278	G	DNM3L_HUMAN	Polymorphism	7354779	A	G	278	G

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_051962	R	278	G	DNM3L_HUMAN	Polymorphism	7354779	C	G	278	G

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADD	PS51533	ADD domain profile.	DNM3L_HUMAN	41-173	3	A:41-173 B:41-173 C:41-173

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADD	PS51533	ADD domain profile.	DNM3L_HUMAN	41-173	1	- B:41-173 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADD	PS51533	ADD domain profile.	DNM3L_HUMAN	41-173	1	A:41-173 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADD	PS51533	ADD domain profile.	DNM3L_HUMAN	41-173	1	- - C:41-173

(no "Exon" information available for 2PVC)

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:347
 aligned with DNM3L_HUMAN | Q9UJW3 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:347
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       
          DNM3L_HUMAN    34 GRDLIAYEVKANQRNIEDICICCGSLQVHTQHPLFEGGICAPCKDKFLDALFLYDDDGYQSYCSICCSGETLLICGNPDCTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPSSRSGLLQRRRKWRSQLKAFYDRESENPLEMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKLAAKWPTKLVKNCFLPLREYFKYFST 380
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...hhhhh..........ee......eehhhhhhhhhh......................eee..........hhhhhhhhh..hhhhhhhhh............ee..ee...hhhhhhhhhhhhhh..........hhhhh....eeee...hhhhhhhh...........eeee......hhhhhhhh....eeeee...........hhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhh....ee..ee....eee..eeee.............hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------ADD  PDB: A:41-173 UniProt: 41-173                                                                                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pvc A  34 GRDLIAYEVKANQRNIEDICICCGSLQVHTQHPLFEGGICAPCKDKFLDALFLYDDDGYQSYCSICCSGETLLICGNPDCTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPSSRSGLLQRRRKWRSQLKAFYDRESENPLEMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPGPFFWMFVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKLAAKWPTKLVKNCFLPLREYFKYFST 380
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373

Chain B from PDB  Type:PROTEIN  Length:347
 aligned with DNM3L_HUMAN | Q9UJW3 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:347
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       
          DNM3L_HUMAN    34 GRDLIAYEVKANQRNIEDICICCGSLQVHTQHPLFEGGICAPCKDKFLDALFLYDDDGYQSYCSICCSGETLLICGNPDCTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPSSRSGLLQRRRKWRSQLKAFYDRESENPLEMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKLAAKWPTKLVKNCFLPLREYFKYFST 380
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...hhhhh....................hhhhhhhhhhh.....................eee........eeehhhhhhhhh..hhhhhhhh............ee..ee...hhhhhhhhhhhhhh..........hhhhh....eeee....hhhhhhh...........eeee......hhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhh.....eeee....eeeeeeeee.............hhhhhhhhh.............hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------ADD  PDB: B:41-173 UniProt: 41-173                                                                                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pvc B  34 GRDLIAYEVKANQRNIEDICICCGSLQVHTQHPLFEGGICAPCKDKFLDALFLYDDDGYQSYCSICCSGETLLICGNPDCTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPSSRSGLLQRRRKWRSQLKAFYDRESENPLEMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPGPFFWMFVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKLAAKWPTKLVKNCFLPLREYFKYFST 380
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373

Chain C from PDB  Type:PROTEIN  Length:347
 aligned with DNM3L_HUMAN | Q9UJW3 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:347
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       
          DNM3L_HUMAN    34 GRDLIAYEVKANQRNIEDICICCGSLQVHTQHPLFEGGICAPCKDKFLDALFLYDDDGYQSYCSICCSGETLLICGNPDCTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPSSRSGLLQRRRKWRSQLKAFYDRESENPLEMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPRPFFWMFVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKLAAKWPTKLVKNCFLPLREYFKYFST 380
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...hhhhh..........ee......eehhhhhhhhhhh.....................eee........ee.hhhhhhh...hhhhhhhh.............ee..ee...hhhhhhhhhhhhhh...................eeee....hhhhhh............eeee..................eeeee............hhhhhhhhhhhhh...........eeeeee....hhhhhhhhhhhhh...eeeeee....eeeeeeeee.............hhhhhhhhhhhhh.................hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------ADD  PDB: C:41-173 UniProt: 41-173                                                                                                   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pvc C  34 GRDLIAYEVKANQRNIEDICICCGSLQVHTQHPLFEGGICAPCKDKFLDALFLYDDDGYQSYCSICCSGETLLICGNPDCTRCYCFECVDSLVGPGTSGKVHAMSNWVCYLCLPSSRSGLLQRRRKWRSQLKAFYDRESENPLEMFETVPVWRRQPVRVLSLFEDIKKELTSLGFLESGSDPGQLKHVVDVTDTVRKDVEEWGPFDLVYGATPPLGHTCDRPPSWYLFQFHRLLQYARPKPGSPGPFFWMFVDNLVLNKEDLDVASRFLEMEPVTIPDVHGGSLQNAVRVWSNIPAIRSRHWALVSEEELSLLAQNKQSSKLAAKWPTKLVKNCFLPLREYFKYFST 380
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373

Chain D from PDB  Type:PROTEIN  Length:7
                                       
               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 ------- Transcript
                 2pvc D 501 ARTKQTA 507

Chain E from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .eee... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 2pvc E 501 ARTKQTA 507

Chain F from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ..ee... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 2pvc F 501 ARTKQTA 507

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 2PVC)

(no "CATH Domain" information available for 2PVC)

(no "Pfam Domain" information available for 2PVC)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (DNM3L_HUMAN | Q9UJW3)

molecular function
	GO:0008047	enzyme activator activity	Binds to and increases the activity of an enzyme.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0030234	enzyme regulator activity	Binds to and modulates the activity of an enzyme.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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).
biological process
	GO:0006306	DNA methylation	The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	GO:0050790	regulation of catalytic activity	Any process that modulates the activity of an enzyme.
	GO:0006349	regulation of gene expression by genetic imprinting	Heritable alterations in the activity of a gene that depend on whether it passed through the paternal or the maternal germline, but that are not encoded by DNA itself.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2pvc)

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	2pvc
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	DNM3L_HUMAN \| Q9UJW3	:	2pv0 2qrv 4u7p 4u7t

2pv0	DNMT3L APO-STRUCTURE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 9)

Sites (9, 9)

SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 3)

PROSITE Motifs (1, 3)

Exons (0, 0)

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Related Entries Specified in the PDB File