3KMT - JenaLib

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Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF VSET/SAH/H3 TERNARY COMPLEX

Authors :   H. Wei, M. M. Zhou

Date :   11 Nov 09 (Deposition) - 10 Nov 10 (Release) - 10 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.78

Chains :   Asym. Unit : A,B,C,G,H,I
Biol. Unit 1: A,G  (1x)
Biol. Unit 2: B,H  (1x)
Biol. Unit 3: C,I  (1x)
Biol. Unit 4: A,B,G,H  (1x)
Biol. Unit 5: C,I  (2x)

Keywords :   Set Domain, Ternary Complex, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Wei, M. M. Zhou
Dimerization Of A Viral Set Protein Endows Its Function.
Proc. Natl. Acad. Sci. Usa V. 107 18433 2010
PubMed-ID: 20937900 | Reference-DOI: 10.1073/PNAS.1009911107

Molecule 1 - A612L PROTEIN
	Chains	:	A, B, C
	Organism Common	:	PBCV-1
	Organism Scientific	:	PARAMECIUM BURSARIA CHLORELLA VIRUS 1
	Organism Taxid	:	10506

Molecule 2 - HISTONE H3
	Chains	:	G, H, I
	Fragment	:	RESIDUES 26-33
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	G	H	I
Biological Unit 1 (1x)	:	A			G
Biological Unit 2 (1x)	:		B			H
Biological Unit 3 (1x)	:			C			I
Biological Unit 4 (1x)	:	A	B		G	H
Biological Unit 5 (2x)	:			C			I

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	MLZ	3	Mod. Amino Acid	N-METHYL-LYSINE
2	SAH	3	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MLZ	1	Mod. Amino Acid	N-METHYL-LYSINE
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MLZ	1	Mod. Amino Acid	N-METHYL-LYSINE
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	MLZ	1	Mod. Amino Acid	N-METHYL-LYSINE
2	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 4 (2, 4)

No.	Name	Count	Type	Full Name
1	MLZ	2	Mod. Amino Acid	N-METHYL-LYSINE
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Biological Unit 5 (2, 4)

No.	Name	Count	Type	Full Name
1	MLZ	2	Mod. Amino Acid	N-METHYL-LYSINE
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:13 , GLY A:14 , GLY A:15 , TYR A:16 , ASP A:49 , TYR A:50 , ILE A:67 , ASN A:69 , HIS A:70 , TYR A:105 , TYR A:109 , TRP A:110 , THR A:117 , ASN A:119 , HOH A:128 , HOH A:136 , HOH A:148 , HOH A:159 , HOH A:175 , MLZ G:27	BINDING SITE FOR RESIDUE SAH A 120
2	AC2	SOFTWARE	LEU B:13 , GLY B:14 , GLY B:15 , TYR B:16 , ASP B:49 , TYR B:50 , ILE B:67 , ASN B:69 , HIS B:70 , TYR B:105 , TYR B:109 , TRP B:110 , THR B:117 , ASN B:119 , HOH B:124 , HOH B:127 , MLZ H:27	BINDING SITE FOR RESIDUE SAH B 120
3	AC3	SOFTWARE	LYS A:26 , HOH A:160 , LEU C:13 , GLY C:14 , GLY C:15 , TYR C:16 , ASP C:49 , TYR C:50 , ILE C:67 , ASN C:69 , HIS C:70 , TYR C:105 , TYR C:109 , TRP C:110 , THR C:117 , ASN C:119 , HOH C:123 , HOH C:129 , HOH C:148 , HOH C:199 , MLZ I:27	BINDING SITE FOR RESIDUE SAH C 120

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

(no "Cis Peptide Bond" information available for 3KMT)

(no "SAP(SNP)/Variant" information available for 3KMT)

(no "PROSITE Motif" information available for 3KMT)

Asymmetric Unit (1, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000359303	2b	ENSE00001974165	chr6:27858570-27858160	411	H31_HUMAN	1-136	136	3	G:25-32 H:25-32 I:25-32	8 8 8

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:119
 aligned with O41094_PBCV1 | O41094 from UniProtKB/TrEMBL  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         O41094_PBCV1     1 MFNDRVIVKKSPLGGYGVFARKSFEKGELVEECLCIVRHNDDWGTALEDYLFSRKNMSAMALGFGAIFNHSKDPNARHELTAGLKRMRIFTIKPIAIGEEITISYGDDYWLSRPRLTQN 119
               SCOP domains d3kmta_ A: Viral histone H3 Lysine 27 Methyltransferase                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....eeeee........eeeeeeeeeee.hhh........eee..eeeee.......ee.....eeeee.hhh.eeeeee........eeee..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3kmt A   1 MFNDRVIVKKSPLGGYGVFARKSFEKGELVEECLCIVRHNDDWGTALEDYLFSRKNMSAMALGFGAIFNHSKDPNARHELTAGLKRMRIFTIKPIAIGEEITISYGDDYWLSRPRLTQN 119
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with O41094_PBCV1 | O41094 from UniProtKB/TrEMBL  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         O41094_PBCV1     1 MFNDRVIVKKSPLGGYGVFARKSFEKGELVEECLCIVRHNDDWGTALEDYLFSRKNMSAMALGFGAIFNHSKDPNARHELTAGLKRMRIFTIKPIAIGEEITISYGDDYWLSRPRLTQN 119
               SCOP domains d3kmtb_ B: Viral histone H3 Lysine 27 Methyltransferase                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.....eeeee........eeeeeeeeeee.hhh........eee..eeeee.......ee.....eeeee.....eeeeee........eeee..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3kmt B   1 MFNDRVIVKKSPLGGYGVFARKSFEKGELVEECLCIVRHNDDWGTALEDYLFSRKNMSAMALGFGAIFNHSKDPNARHELTAGLKRMRIFTIKPIAIGEEITISYGDDYWLSRPRLTQN 119
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:119
 aligned with O41094_PBCV1 | O41094 from UniProtKB/TrEMBL  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         O41094_PBCV1     1 MFNDRVIVKKSPLGGYGVFARKSFEKGELVEECLCIVRHNDDWGTALEDYLFSRKNMSAMALGFGAIFNHSKDPNARHELTAGLKRMRIFTIKPIAIGEEITISYGDDYWLSRPRLTQN 119
               SCOP domains d3kmtc_ C: Viral histone H3 Lysine 27 Methyltransferase                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------SET-3kmtC01 C:43-106                                            ------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------SET-3kmtC02 C:43-106                                            ------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------SET-3kmtC03 C:43-106                                            ------------- Pfam domains (3)
         Sec.struct. author .....eeeee.....eeeee........eeeeeeeeeee.hhh........eee..eeeee.......ee.....eeeee.hhh.eeeeee........eeee..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3kmt C   1 MFNDRVIVKKSPLGGYGVFARKSFEKGELVEECLCIVRHNDDWGTALEDYLFSRKNMSAMALGFGAIFNHSKDPNARHELTAGLKRMRIFTIKPIAIGEEITISYGDDYWLSRPRLTQN 119
                                    10        20        30        40        50        60        70        80        90       100       110

Chain G from PDB  Type:PROTEIN  Length:8
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:8
            H31_HUMAN    26 ARKSAPAT  33
               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 1.2b     Transcript 1
                 3kmt G  25 ARkSAPAT  32
                              |     
                              |     
                             27-MLZ

Chain H from PDB  Type:PROTEIN  Length:8
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:8
            H31_HUMAN    26 ARKSAPAT  33
               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 1.2b     Transcript 1
                 3kmt H  25 ARkSAPAT  32
                              |     
                             27-MLZ

Chain I from PDB  Type:PROTEIN  Length:8
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:8
            H31_HUMAN    26 ARKSAPAT  33
               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 1.2b     Transcript 1
                 3kmt I  25 ARkSAPAT  32
                              |     
                             27-MLZ

Legend:		→ Mismatch	(orange background)
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	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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-clip (280)

Superfamily: SET domain (44)

Family: Viral histone H3 Lysine 27 Methyltransferase (5)

Protein domain: Viral histone H3 Lysine 27 Methyltransferase (5)

Paramecium bursaria chlorella virus 1, PBCV-1 [TaxId: 10506] (5)

1a	d3kmta_	A:
1b	d3kmtb_	B:
1c	d3kmtc_	C:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: SET] (46)

Family: SET (46)

Paramecium bursaria Chlorella virus 1 (PBCV-1) (4)

1a	SET-3kmtC01	C:43-106
1b	SET-3kmtC02	C:43-106
1c	SET-3kmtC03	C:43-106

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (O41094_PBCV1 | O41094)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.

Chain G,H,I (H31_HUMAN | P68431)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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:0006335	DNA replication-dependent nucleosome assembly	The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
	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: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:0002230	positive regulation of defense response to virus by host	Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
	GO:0045815	positive regulation of gene expression, epigenetic	Any epigenetic process that activates or increases the rate of gene expression.
	GO:0051290	protein heterotetramerization	The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
	GO:0060968	regulation of gene silencing	Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation.
	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.
	GO:0098792	xenophagy	The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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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3kma	CRYSTAL STRUCTURE OF VSET UNDER CONDITION A
3kmj	CRYSTAL STRUCTURE OF VSET UNDER CONDITION B

Description

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Ligands, Modified Residues, Ions (2, 6)

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