3LQI - 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)

Title :   CRYSTAL STRUCTURE OF MLL1 PHD3-BROMO COMPLEXED WITH H3(1-9)K4ME2 PEPTIDE

Authors :   Z. Wang, D. J. Patel

Date :   09 Feb 10 (Deposition) - 07 Jul 10 (Release) - 28 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.92

Chains :   Asym. Unit : A,B,C,R,S,T
Biol. Unit 1: A,R  (1x)
Biol. Unit 2: B,S  (1x)
Biol. Unit 3: C,T  (1x)

Keywords :   Phd Finger, Bromodomain, Mll1, Leukemia, H3(1-9)K4Me2, Chromosomal Protein, Dna-Binding, Nucleosome Core, Nucleus, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Wang, J. Song, T. A. Milne, G. G. Wang, H. Li, C. D. Allis, D. J. Patel
Pro Isomerization In Mll1 Phd3-Bromo Cassette Connects H3K4Me Readout To Cyp33 And Hdac-Mediated Repression.
Cell(Cambridge, Mass. ) V. 141 1183 2010
PubMed-ID: 20541251 | Reference-DOI: 10.1016/J.CELL.2010.05.016

Molecule 1 - MLL1 PHD3-BROMO
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSFDUET-1
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	THIRD PHD FINGER AND BROMODOMAIN OF MLL1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - HISTONE H3
	Chains	:	R, S, T
	Engineered	:	YES
	Fragment	:	HISTONE H3 N-TERMINAL TAIL
	Other Details	:	THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	R	S	T
Biological Unit 1 (1x)	:	A			R
Biological Unit 2 (1x)	:		B			S
Biological Unit 3 (1x)	:			C			T

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	MLY	3	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MLY	1	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MLY	1	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	MLY	1	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:1569 , CYS A:1572 , HIS A:1596 , CYS A:1599	BINDING SITE FOR RESIDUE ZN A 1
2	AC2	SOFTWARE	CYS A:1588 , CYS A:1591 , CYS A:1621 , CYS A:1624	BINDING SITE FOR RESIDUE ZN A 2
3	AC3	SOFTWARE	CYS B:1569 , CYS B:1572 , HIS B:1596 , CYS B:1599	BINDING SITE FOR RESIDUE ZN B 3
4	AC4	SOFTWARE	CYS B:1588 , CYS B:1591 , CYS B:1621 , CYS B:1624	BINDING SITE FOR RESIDUE ZN B 4
5	AC5	SOFTWARE	CYS C:1569 , CYS C:1572 , HIS C:1596 , CYS C:1599	BINDING SITE FOR RESIDUE ZN C 5
6	AC6	SOFTWARE	CYS C:1588 , CYS C:1591 , CYS C:1621 , CYS C:1624	BINDING SITE FOR RESIDUE ZN C 6

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

Asymmetric Unit

No.	Residues
1	His A:1628	-	Pro A:1629
2	His B:1628	-	Pro B:1629
3	His C:1628	-	Pro C:1629

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

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	KMT2A_HUMAN	1431-1482 1479-1533 1566-1627	3	- - A:1566-1627 B:1566-1627 C:1566-1627
2	BROMODOMAIN_2	PS50014	Bromodomain profile.	KMT2A_HUMAN	1703-1748	3	A:1704-1748 B:1704-1748 C:1703-1748

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	KMT2A_HUMAN	1431-1482 1479-1533 1566-1627	1	- - A:1566-1627 - -
2	BROMODOMAIN_2	PS50014	Bromodomain profile.	KMT2A_HUMAN	1703-1748	1	A:1704-1748 - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	KMT2A_HUMAN	1431-1482 1479-1533 1566-1627	1	- - - B:1566-1627 -
2	BROMODOMAIN_2	PS50014	Bromodomain profile.	KMT2A_HUMAN	1703-1748	1	- B:1704-1748 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZF_PHD_2	PS50016	Zinc finger PHD-type profile.	KMT2A_HUMAN	1431-1482 1479-1533 1566-1627	1	- - - - C:1566-1627
2	BROMODOMAIN_2	PS50014	Bromodomain profile.	KMT2A_HUMAN	1703-1748	1	- - C:1703-1748

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	R:1-6 S:1-7 T:1-9	6 7 9

2.1a	ENST00000389506	1a	ENSE00002162629	chr11:118307205-118307659	455	KMT2A_HUMAN	-	0	0	-	-
2.5b	ENST00000389506	5b	ENSE00001633768	chr11:118339490-118339559	70	KMT2A_HUMAN	-	0	0	-	-
2.6a	ENST00000389506	6a	ENSE00001610993	chr11:118342377-118345030	2654	KMT2A_HUMAN	1-298	298	0	-	-
2.7b	ENST00000389506	7b	ENSE00002192425	chr11:118347520-118347697	178	KMT2A_HUMAN	299-358	60	0	-	-
2.8a	ENST00000389506	8a	ENSE00001785290	chr11:118348682-118348916	235	KMT2A_HUMAN	358-436	79	0	-	-
2.9b	ENST00000389506	9b	ENSE00002148387	chr11:118350889-118350953	65	KMT2A_HUMAN	436-451	16	0	-	-
2.10a	ENST00000389506	10a	ENSE00001660587	chr11:118352430-118352807	378	KMT2A_HUMAN	-	0	0	-	-
2.11	ENST00000389506	11	ENSE00001619243	chr11:118353137-118353210	74	KMT2A_HUMAN	-	0	0	-	-
2.12a	ENST00000389506	12a	ENSE00001735103	chr11:118354898-118355029	132	KMT2A_HUMAN	-	0	0	-	-
2.13	ENST00000389506	13	ENSE00001703734	chr11:118355577-118355690	114	KMT2A_HUMAN	-	0	0	-	-
2.15	ENST00000389506	15	ENSE00001775852	chr11:118359329-118359475	147	KMT2A_HUMAN	-	0	0	-	-
2.16	ENST00000389506	16	ENSE00001798700	chr11:118360507-118360602	96	KMT2A_HUMAN	-	0	0	-	-
2.17	ENST00000389506	17	ENSE00001621217	chr11:118360844-118360964	121	KMT2A_HUMAN	-	0	0	-	-
2.18a	ENST00000389506	18a	ENSE00001785002	chr11:118361911-118362024	114	KMT2A_HUMAN	-	0	0	-	-
2.19	ENST00000389506	19	ENSE00001611699	chr11:118362459-118362643	185	KMT2A_HUMAN	-	0	0	-	-
2.20b	ENST00000389506	20b	ENSE00001749282	chr11:118363772-118363945	174	KMT2A_HUMAN	-	0	0	-	-
2.21	ENST00000389506	21	ENSE00001625999	chr11:118365003-118365113	111	KMT2A_HUMAN	-	0	0	-	-
2.22	ENST00000389506	22	ENSE00001642774	chr11:118365409-118365482	74	KMT2A_HUMAN	-	0	0	-	-
2.23	ENST00000389506	23	ENSE00001729453	chr11:118366415-118366608	194	KMT2A_HUMAN	-	0	0	-	-
2.24	ENST00000389506	24	ENSE00001671815	chr11:118366976-118367082	107	KMT2A_HUMAN	-	0	0	-	-
2.25a	ENST00000389506	25a	ENSE00001513432	chr11:118368651-118368723	73	KMT2A_HUMAN	-	0	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:176
 aligned with KMT2A_HUMAN | Q03164 from UniProtKB/Swiss-Prot  Length:3969

    Alignment length:214
                                  1574      1584      1594      1604      1614      1624      1634      1644      1654      1664      1674      1684      1694      1704      1714      1724      1734      1744      1754      1764      1774    
         KMT2A_HUMAN   1565 KGNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHPAEWRLALEKELQISLKQVLTALLNSRTTSHLLRYRQAAKPPDLNPETEESIPSRSSPEGPDPPVLTEVSKQDDQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVKKSRFWE 1778
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee......eee.......eee......eee.hhhh.hhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...--------------------------------------...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ZF_PHD_2  PDB: A:1566-1627 UniProt: 1566-1627                 ---------------------------------------------------------------------------BROMODOMAIN_2  PDB: A:1704-1748               ------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3lqi A 1565 SGNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHPAEWRLALEKELQISLKQVLTALLNSRTTSHLLRYRQ--------------------------------------QPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVKKSRFWE 1778
                                  1574      1584      1594      1604      1614      1624      1634      1644      1654      1664|        -         -         -      1704      1714      1724      1734      1744      1754      1764      1774    
                                                                                                                             1665                                   1704

Chain B from PDB  Type:PROTEIN  Length:177
 aligned with KMT2A_HUMAN | Q03164 from UniProtKB/Swiss-Prot  Length:3969

    Alignment length:215
                                  1574      1584      1594      1604      1614      1624      1634      1644      1654      1664      1674      1684      1694      1704      1714      1724      1734      1744      1754      1764      1774     
         KMT2A_HUMAN   1565 KGNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHPAEWRLALEKELQISLKQVLTALLNSRTTSHLLRYRQAAKPPDLNPETEESIPSRSSPEGPDPPVLTEVSKQDDQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVKKSRFWEP 1779
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee......eee.......eee......eee.hhhh.hhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...--------------------------------------...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ZF_PHD_2  PDB: B:1566-1627 UniProt: 1566-1627                 ---------------------------------------------------------------------------BROMODOMAIN_2  PDB: B:1704-1748               ------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3lqi B 1565 SGNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHPAEWRLALEKELQISLKQVLTALLNSRTTSHLLRYRQ--------------------------------------QPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVKKSRFWEP 1779
                                  1574      1584      1594      1604      1614      1624      1634      1644      1654      1664|        -         -         -      1704      1714      1724      1734      1744      1754      1764      1774     
                                                                                                                             1665                                   1704

Chain C from PDB  Type:PROTEIN  Length:181
 aligned with KMT2A_HUMAN | Q03164 from UniProtKB/Swiss-Prot  Length:3969

    Alignment length:220
                                  1574      1584      1594      1604      1614      1624      1634      1644      1654      1664      1674      1684      1694      1704      1714      1724      1734      1744      1754      1764      1774      1784
         KMT2A_HUMAN   1565 KGNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHPAEWRLALEKELQISLKQVLTALLNSRTTSHLLRYRQAAKPPDLNPETEESIPSRSSPEGPDPPVLTEVSKQDDQQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVKKSRFWEPNKVSS 1784
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee......eee.......eee......eee.hhhh.hhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------------------------------....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ZF_PHD_2  PDB: C:1566-1627 UniProt: 1566-1627                 ---------------------------------------------------------------------------BROMODOMAIN_2  PDB: C:1703-1748               ------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3lqi C 1565 SGNFCPLCDKCYDDDDYESKMMQCGKCDRWVHSKCENLSDEMYEILSNLPESVAYTCVNCTERHPAEWRLALEKELQISLKQVLTALLNSRTTSHLLRY---------------------------------------QQPLDLEGVKRKMDQGNYTSVLEFSDDIVKIIQAAINSDGGQPEIKKANSMVKSFFIRQMERVFPWFSVKKSRFWEPNKVSS 1784
                                  1574      1584      1594      1604      1614      1624      1634      1644      1654        |-         -         -         -      1704      1714      1724      1734      1744      1754      1764      1774      1784
                                                                                                                           1663                                    1703

Chain R from PDB  Type:PROTEIN  Length:6
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:6
           H31_HUMAN      2 ARTKQT    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 1 1.2b   Transcript 1
                3lqi R    1 ARTkQT    6
                               |  
                               |  
                               4-MLY

Chain S from PDB  Type:PROTEIN  Length:7
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:7
           H31_HUMAN      2 ARTKQTA    8
               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
                3lqi S    1 ARTkQTA    7
                               |   
                               4-MLY

Chain T from PDB  Type:PROTEIN  Length:9
 aligned with H31_HUMAN | P68431 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:9
           H31_HUMAN      2 ARTKQTARK   10
               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 1 Exon 1.2b Transcript 1
                3lqi T    1 ARTkQTARK    9
                               |     
                               4-MLY

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 3LQI)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (KMT2A_HUMAN | Q03164)

molecular function
	GO:0003680	AT DNA binding	Interacting selectively and non-covalently with oligo(A) and oligo(T) tracts of DNA (AT DNA).
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0001046	core promoter sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.
	GO:0042800	histone methyltransferase activity (H3-K4 specific)	Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein.
	GO:0018024	histone-lysine N-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0070577	lysine-acetylated histone binding	Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0045322	unmethylated CpG binding	Interacting selectively and non-covalently with unmethylated CpG motifs. Unmethylated CpG dinucleotides are often associated with gene promoters.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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:0009952	anterior/posterior pattern specification	The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0032922	circadian regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
	GO:0050890	cognition	The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
	GO:0060216	definitive hemopoiesis	A second wave of blood cell production that, in vertebrates, generates long-term hemopoietic stem cells that continously provide erythroid, myeloid and lymphoid lineages throughout adulthood.
	GO:0035162	embryonic hemopoiesis	The stages of blood cell formation that take place within the embryo.
	GO:0035640	exploration behavior	The specific behavior of an organism in response to a novel environment or stimulus.
	GO:0044648	histone H3-K4 dimethylation	The modification of histone H3 by addition of two methyl groups to lysine at position 4 of the histone.
	GO:0051568	histone H3-K4 methylation	The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.
	GO:0080182	histone H3-K4 trimethylation	The modification of histone H3 by addition of three methyl groups to lysine at position 4 of the histone.
	GO:0043984	histone H4-K16 acetylation	The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 16 of the histone.
	GO:0048873	homeostasis of number of cells within a tissue	Any biological process involved in the maintenance of the steady-state number of cells within a population of cells in a tissue.
	GO:0051899	membrane depolarization	The process in which membrane potential decreases with respect to its steady-state potential, usually from negative potential to a more positive potential. For example, the initial depolarization during the rising phase of an action potential is in the direction from the negative steady-state resting potential towards the positive membrane potential that will be the peak of the action potential.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0018026	peptidyl-lysine monomethylation	The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine.
	GO:2001040	positive regulation of cellular response to drug	Any process that activates or increases the frequency, rate or extent of cellular response to drug.
	GO:0051571	positive regulation of histone H3-K4 methylation	Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
	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:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0032411	positive regulation of transporter activity	Any process that activates or increases the activity of a transporter.
	GO:0009791	post-embryonic development	The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
	GO:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0071440	regulation of histone H3-K14 acetylation	Any process that modulates the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone.
	GO:1901674	regulation of histone H3-K27 acetylation	Any process that modulates the frequency, rate or extent of histone H3-K27 acetylation.
	GO:0051569	regulation of histone H3-K4 methylation	Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
	GO:2000615	regulation of histone H3-K9 acetylation	Any process that modulates the frequency, rate or extent of histone H3-K9 acetylation.
	GO:0048172	regulation of short-term neuronal synaptic plasticity	A process that modulates short-term neuronal synaptic plasticity, the ability of neuronal synapses to change in the short-term as circumstances require. Short-term neuronal synaptic plasticity generally involves increasing or decreasing synaptic sensitivity.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0009416	response to light stimulus	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 light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
	GO:0035864	response to potassium ion	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 potassium ion stimulus.
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	GO:0048536	spleen development	The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0008542	visual learning	Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
	GO:0071339	MLL1 complex	A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0035097	histone methyltransferase complex	A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

Chain R,S,T (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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	3lqi
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	H31_HUMAN \| P68431
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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PROSITE Motifs (2, 6)

Exons (1, 3)

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Gene Ontology (84, 88)

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