3Q6S - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF THE HETEROCHROMATIN PROTEIN 1 BETA CHROMOSHADOW DOMAIN COMPLEXED WITH A PEPTIDE FROM SHUGOSHIN 1

Authors :   C. A. Brautigam, J. Chaudhary, H. Yu

Date :   03 Jan 11 (Deposition) - 14 Dec 11 (Release) - 13 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

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

Keywords :   Incenp, Heterochromatin, Centromere, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Kang, J. Chaudhary, H. Dong, S. Kim, C. A. Brautigam, H. Yu
Mitotic Centromeric Targeting Of Hp1 And Its Binding To Sgo Are Dispensable For Sister-Chromatid Cohesion In Human Cells.
Mol Biol Cell V. 22 1181 2011
PubMed-ID: 21346195 | Reference-DOI: 10.1091/MBC.E11-01-0009

Molecule 1 - CHROMOBOX PROTEIN HOMOLOG 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CHROMOSHADOW DOMAIN, RESIDUES 108-185
	Gene	:	CBX1, CBX
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HP1HSBETA, HETEROCHROMATIN PROTEIN 1 HOMOLOG BETA, HP1 BETA, HETEROCHROMATIN PROTEIN P25, M31, MODIFIER 1 PROTEIN, P25BETA

Molecule 2 - SHUGOSHIN-LIKE 1
	Chains	:	E, F
	Engineered	:	YES
	Fragment	:	RESIDUES 445-463
	Other Details	:	CHEMICALLY SYNTHESIZED PEPTIDE
	Synonym	:	HSGO1, SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-85
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3Q6S)

(no "Site" information available for 3Q6S)

(no "SS Bond" information available for 3Q6S)

Asymmetric Unit

No.	Residues
1	Tyr B:173	-	Pro B:174
2	Tyr D:173	-	Pro D:174

(no "SAP(SNP)/Variant" information available for 3Q6S)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CBX1_HUMAN	21-79 117-175	4	- A:117-174 B:117-175 C:117-173 D:117-174

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CBX1_HUMAN	21-79 117-175	2	- A:117-174 - - D:117-174

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHROMO_2	PS50013	Chromo and chromo shadow domain profile.	CBX1_HUMAN	21-79 117-175	2	- - B:117-175 C:117-173 -

Asymmetric Unit (2, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2	ENST00000393408	2	ENSE00001515177	chr17:46178560-46178117	444	CBX1_HUMAN	-	0	0	-	-
1.5	ENST00000393408	5	ENSE00002178956	chr17:46154403-46154227	177	CBX1_HUMAN	1-47	47	0	-	-
1.6a	ENST00000393408	6a	ENSE00000735652	chr17:46153540-46153363	178	CBX1_HUMAN	47-106	60	0	-	-
1.7b	ENST00000393408	7b	ENSE00000735651	chr17:46152462-46152368	95	CBX1_HUMAN	107-138	32	4	A:109-138 B:109-138 C:110-138 D:110-138	30 30 29 29
1.8c	ENST00000393408	8c	ENSE00001824299	chr17:46148941-46147414	1528	CBX1_HUMAN	138-185	48	4	A:138-174 B:138-175 C:138-173 D:138-174	37 38 36 37

Asymmetric Unit

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

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:66
 aligned with CBX1_HUMAN | P83916 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:66
                                   118       128       138       148       158       168      
           CBX1_HUMAN   109 KPRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYP 174
               SCOP domains d3q6sa_ A: Heterochromatin protein 1, HP1                          SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh..eeeeeeee......eeeeee.....eeeeehhhhhhhhhhhhhhhhhh.eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------CHROMO_2  PDB: A:117-174 UniProt: 117-175                  PROSITE
           Transcript 1 (1) Exon 1.7b  PDB: A:109-138     ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.8c  PDB: A:138-174             Transcript 1 (2)
                 3q6s A 109 KPRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYP 174
                                   118       128       138       148       158       168

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with CBX1_HUMAN | P83916 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:67
                                   118       128       138       148       158       168       
           CBX1_HUMAN   109 KPRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPS 175
               SCOP domains d3q6sb_ B: Heterochromatin protein 1, HP1                           SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..eeeeeeee......eeeeee......eeeehhhhhhhhhhhhhhhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------CHROMO_2  PDB: B:117-175 UniProt: 117-175                   PROSITE
           Transcript 1 (1) Exon 1.7b  PDB: B:109-138     ------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.8c  PDB: B:138-175 [INCOMPLETE] Transcript 1 (2)
                 3q6s B 109 KPRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYPS 175
                                   118       128       138       148       158       168

Chain C from PDB  Type:PROTEIN  Length:64
 aligned with CBX1_HUMAN | P83916 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:64
                                   119       129       139       149       159       169    
           CBX1_HUMAN   110 PRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSY 173
               SCOP domains d3q6sc_ C: Heterochromatin protein 1, HP1                        SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeeeeeeee..eeeeeeee......eeeehhhhhhhhhhhhhhhhhh.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------CHROMO_2  PDB: C:117-173 UniProt: 117-175                 PROSITE
           Transcript 1 (1) Exon 1.7b  PDB: C:110-138    ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.8c  PDB: C:138-173            Transcript 1 (2)
                 3q6s C 110 PRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSY 173
                                   119       129       139       149       159       169

Chain D from PDB  Type:PROTEIN  Length:65
 aligned with CBX1_HUMAN | P83916 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:65
                                   119       129       139       149       159       169     
           CBX1_HUMAN   110 PRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYP 174
               SCOP domains d3q6sd_ D: Heterochromatin protein 1, HP1                         SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..eeeeeeee......eeeeee......eeeehhhhhhhhhhhhhhhhhhheeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------CHROMO_2  PDB: D:117-174 UniProt: 117-175                  PROSITE
           Transcript 1 (1) Exon 1.7b  PDB: D:110-138    ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.8c  PDB: D:138-174             Transcript 1 (2)
                 3q6s D 110 PRGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWHSYP 174
                                   119       129       139       149       159       169

Chain E from PDB  Type:PROTEIN  Length:14
 aligned with SGO1_HUMAN | Q5FBB7 from UniProtKB/Swiss-Prot  Length:561

    Alignment length:14
                                   455    
           SGO1_HUMAN   446 NVSLYPVVKIRRLS 459
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author ..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 3q6s E 446 NVSLYPVVKIRRLS 459
                                   455

Chain F from PDB  Type:PROTEIN  Length:16
 aligned with SGO1_HUMAN | Q5FBB7 from UniProtKB/Swiss-Prot  Length:561

    Alignment length:16
                                   454      
           SGO1_HUMAN   445 TNVSLYPVVKIRRLSL 460
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 3q6s F 445 TNVSLYPVVKIRRLSL 460
                                   454

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: Chromo domain-like (82)

Family: Chromo domain (41)

Protein domain: Heterochromatin protein 1, HP1 (11)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d3q6sa_	A:
1b	d3q6sb_	B:
1c	d3q6sc_	C:
1d	d3q6sd_	D:

(no "CATH Domain" information available for 3Q6S)

(no "Pfam Domain" information available for 3Q6S)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CBX1_HUMAN | P83916)

molecular function
	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:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:1990226	histone methyltransferase binding	Interacting selectively and non-covalently with a histone methyltransferase enzyme.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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.
biological process
	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.
cellular component
	GO:0000785	chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
	GO:0010369	chromocenter	A region in which centric, heterochromatic portions of one or more chromosomes form a compact structure.
	GO:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0001939	female pronucleus	The pronucleus originating from the ovum that is being fertilized.
	GO:0001940	male pronucleus	The pronucleus originating from the spermatozoa that was involved in fertilization.
	GO:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005720	nuclear heterochromatin	A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
	GO: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.
	GO:0005721	pericentric heterochromatin	Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
	GO:0005819	spindle	The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

Chain E,F (SGO1_HUMAN | Q5FBB7)

molecular function
	GO:0019900	kinase binding	Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
	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:0008608	attachment of spindle microtubules to kinetochore	The process in which spindle microtubules become physically associated with the proteins making up the kinetochore complex.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0010457	centriole-centriole cohesion	The cell cycle process in which the two centrioles within a centrosome remain tightly paired.
	GO:0007059	chromosome segregation	The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
	GO:0045132	meiotic chromosome segregation	The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle.
	GO:0007062	sister chromatid cohesion	The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
cellular component
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0000777	condensed chromosome kinetochore	A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
	GO:0000779	condensed chromosome, centromeric region	The region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0000780	condensed nuclear chromosome, centromeric region	The region of a condensed nuclear chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0000776	kinetochore	A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	GO:0030892	mitotic cohesin complex	A cohesin complex that mediates sister chromatid cohesion during mitosis; has a subunit composition distinct from that of the meiotic cohesin complex.
	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.
	GO:0000922	spindle pole	Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

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(no "Sites" information available for 3q6s)

	Cis Peptide Bonds
		Tyr B:173 - Pro B:174	[ RasMol ]
		Tyr D:173 - Pro D:174	[ RasMol ]

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	3q6s
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	CBX1_HUMAN \| P83916	:	1guw 1s4z 2fmm 3f2u 5t1g
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(no "Related Entries Specified in the PDB File" available for 3Q6S)

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