4W5A - JenaLib

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Title :   COMPLEX STRUCTURE OF ATRX ADD BOUND TO H3K9ME3S10PH PEPTIDE

Authors :   D. Zhao, B. Xiang, H. Li

Date :   17 Aug 14 (Deposition) - 21 Jan 15 (Release) - 17 Jun 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Epigenetic Regulation, Complex, Transcription, Mitosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. M. Noh, I. Maze, D. Zhao, B. Xiang, W. Wenderski, P. W. Lewis, L. Shen, H. Li, C. D. Allis
Atrx Tolerates Activity-Dependent Histone H3 Methyl/Phos Switching To Maintain Repetitive Element Silencing In Neurons
Proc. Natl. Acad. Sci. Usa V. 112 6820 2015
PubMed-ID: 25538301 | Reference-DOI: 10.1073/PNAS.1411258112

Molecule 1 - TRANSCRIPTIONAL REGULATOR ATRX
	Chains	:	A, B, E
	EC Number	:	3.6.4.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGOOD6P
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 167-289
	Gene	:	ATRX, RAD54L, XH2
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ATP-DEPENDENT HELICASE ATRX,X-LINKED HELICASE II,X-LINKED NUCLEAR PROTEIN,XNP,ZNF-HX

Molecule 2 - PEPTIDE FROM HISTONE H3.3
	Chains	:	C, D, F
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	M3L	3	Mod. Amino Acid	N-TRIMETHYLLYSINE
2	SEP	3	Mod. Amino Acid	PHOSPHOSERINE
3	ZN	9	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 2)

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

Biological Unit 3 (2, 2)

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

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:11 , CYS A:14 , CYS A:37 , CYS A:40	binding site for residue ZN A 501
2	AC2	SOFTWARE	CYS A:60 , CYS A:63 , CYS A:80 , CYS A:83	binding site for residue ZN A 502
3	AC3	SOFTWARE	CYS A:72 , CYS A:75 , CYS A:105 , CYS A:108	binding site for residue ZN A 503
4	AC4	SOFTWARE	CYS B:11 , CYS B:14 , CYS B:37 , CYS B:40	binding site for residue ZN B 501
5	AC5	SOFTWARE	CYS B:60 , CYS B:63 , CYS B:80 , CYS B:83	binding site for residue ZN B 502
6	AC6	SOFTWARE	CYS B:72 , CYS B:75 , CYS B:105 , CYS B:108	binding site for residue ZN B 503
7	AC7	SOFTWARE	CYS E:11 , CYS E:14 , CYS E:37 , CYS E:40	binding site for residue ZN E 501
8	AC8	SOFTWARE	CYS E:60 , CYS E:63 , CYS E:80 , CYS E:83	binding site for residue ZN E 502
9	AC9	SOFTWARE	CYS E:72 , CYS E:75 , CYS E:105 , CYS E:108	binding site for residue ZN E 503

(no "SS Bond" information available for 4W5A)

Asymmetric Unit

No.	Residues
1	Phe B:21	-	Gln B:22

(no "SAP(SNP)/Variant" information available for 4W5A)

(no "PROSITE Motif" information available for 4W5A)

(no "Exon" information available for 4W5A)

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:128
                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee......ee........ee......eehhhhhhhhhhh....................eeee......eeehhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w5a A   1 GPLGSMGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPEPLLDLVTACNSVYENLE 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........................eee......eeehhhhhhhh......................eeee......eeehhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4w5a B   1 GPLGSMGIVSCTACGQQVNHFQKDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPEPLLDLVTACNSVYEN 126
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeee...... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4w5a C   1 ARTKQTARksT  11
                                    10 
                                    9-M3L
                                    10-SEP

Chain D from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .eeee....... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 4w5a D   1 ARTKQTARksTG  12
                                    10  
                                    9-M3L
                                    10-SEP

Chain E from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee......ee..ee......eehhhhhhhhh......................eeee......eeehhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4w5a E   8 IVSCTACGQQVNIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWCAEGGNLICCDFCHNAFCKKCILRNLGRRELSTIMDENNQWYCYICHPEPLLDLVTACNSVYENL 127
                                    17 ||     33        43        53        63        73        83        93       103       113       123    
                                      19|                                                                                                     
                                       26

Chain F from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eeee...... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4w5a F   1 ARTKQTARksT  11
                                    10 
                                    9-M3L
                                    10-SEP

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 4W5A)

(no "CATH Domain" information available for 4W5A)

(no "Pfam Domain" information available for 4W5A)

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Asymmetric Unit
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	Ligands, Modified Residues, Ions
		M3L	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SEP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Phe B:21 - Gln B:22	[ RasMol ]

Biological Units
	Complete Structure
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		Biological Unit 3	[ Jena3D ]

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3ql9	STRUCTURE OF HUMAN ATRX ADD IN COMPLEX WITH H3K9(1-15)ME3 PEPTIDE IN MONOCLINIC CRYSTAL FORM.
3qla	STRUCTURE OF HUMAN ATRX ADD DOMAIN IN COMPLEX WITH H3K9(1-15)ME3 PEPTIDE IN HEXAGONAL CRYSTAL FORM.
3qlc	STRUCTURE OF HUMAN ATRX ADD IN COMPLEX WITH UNMODIFIED H3(1-15) PEPTIDE.
3qln	STRUCTURE OF HUMAN ATRX ADD IN ITS FREE STATE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (71, 80)

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