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Title :   THE SOLUTION STRUCTURE OF THE KI67FHA/HNIFK(226-269)3P COMPLEX

Authors :   I. -J. L. Byeon, H. Li, H. Song, A. M. Gronenborn, M. D. Tsai

Date :   25 Jul 05 (Deposition) - 25 Oct 05 (Release) - 26 May 10 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (100x)

Keywords :   Ki67; Fha; Nifk; Nmr; Phosphoprotein, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. J. Byeon, H. Li, H. Song, A. M. Gronenborn, M. D. Tsai
Sequential Phosphorylation And Multisite Interactions Characterize Specific Target Recognition By The Fha Domain Of Ki67.
Nat. Struct. Mol. Biol. V. 12 987 2005
PubMed-ID: 16244663 | Reference-DOI: 10.1038/NSMB1008
(for further references see the PDB file header)

Molecule 1 - ANTIGEN KI-67
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PEG
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	FHA DOMAIN
	Gene	:	MKI67
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - MKI67 FHA DOMAIN INTERACTING NUCLEOLAR PHOSPHOPROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PEG
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 226-269
	Gene	:	MKI67IP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NUCLEOLAR PROTEIN INTERACTING WITH THE FHA DOMAIN OF PKI-67


NMR Structure (100x)	:

Summary Information (see also Sequences/Alignments below)

NMR Structure (2, 3)

No.	Name	Count	Type	Full Name
1	SEP	1	Mod. Amino Acid	PHOSPHOSERINE
2	TPO	2	Mod. Amino Acid	PHOSPHOTHREONINE

(no "Site" information available for 2AFF)

(no "SS Bond" information available for 2AFF)

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

(no "SAP(SNP)/Variant" information available for 2AFF)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FHA_DOMAIN	PS50006	Forkhead-associated (FHA) domain profile.	KI67_HUMAN	27-76	1	A:27-76

NMR Structure (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000285814	1a	ENSE00001632880	chr2:122494499-122494322	178	MK67I_HUMAN	1-35	35	0	-	-
1.2b	ENST00000285814	2b	ENSE00001020894	chr2:122493326-122493189	138	MK67I_HUMAN	36-81	46	0	-	-
1.3	ENST00000285814	3	ENSE00001603532	chr2:122489780-122489672	109	MK67I_HUMAN	82-118	37	0	-	-
1.5b	ENST00000285814	5b	ENSE00001732800	chr2:122488680-122488469	212	MK67I_HUMAN	118-188	71	0	-	-
1.6c	ENST00000285814	6c	ENSE00001781306	chr2:122486112-122486053	60	MK67I_HUMAN	189-208	20	0	-	-
1.7	ENST00000285814	7	ENSE00001762164	chr2:122485932-122485864	69	MK67I_HUMAN	209-231	23	1	B:228-231	4
1.8f	ENST00000285814	8f	ENSE00001159639	chr2:122485488-122484521	968	MK67I_HUMAN	232-293	62	1	B:232-267	36

2.1a	ENST00000368654	1a	ENSE00001447684	chr10:129924649-129924363	287	KI67_HUMAN	-	0	0	-	-
2.2a	ENST00000368654	2a	ENSE00001387181	chr10:129924020-129923840	181	KI67_HUMAN	1-31	31	1	A:3-31	29
2.3	ENST00000368654	3	ENSE00000987369	chr10:129921433-129921355	79	KI67_HUMAN	31-57	27	1	A:31-57	27
2.4	ENST00000368654	4	ENSE00000987370	chr10:129921260-129921145	116	KI67_HUMAN	58-96	39	1	A:58-96	39
2.5	ENST00000368654	5	ENSE00000987371	chr10:129917583-129917517	67	KI67_HUMAN	96-118	23	1	A:96-100	5
2.6	ENST00000368654	6	ENSE00000987372	chr10:129914800-129914755	46	KI67_HUMAN	119-134	16	0	-	-
2.7b	ENST00000368654	7b	ENSE00000987373	chr10:129914271-129913192	1080	KI67_HUMAN	134-494	361	0	-	-
2.8	ENST00000368654	8	ENSE00000987374	chr10:129911866-129911691	176	KI67_HUMAN	494-552	59	0	-	-
2.9b	ENST00000368654	9b	ENSE00000987375	chr10:129910709-129910397	313	KI67_HUMAN	553-657	105	0	-	-
2.10	ENST00000368654	10	ENSE00000987376	chr10:129910309-129910191	119	KI67_HUMAN	657-696	40	0	-	-
2.11a	ENST00000368654	11a	ENSE00000987377	chr10:129910080-129909909	172	KI67_HUMAN	697-754	58	0	-	-
2.12	ENST00000368654	12	ENSE00000987378	chr10:129908797-129908642	156	KI67_HUMAN	754-806	53	0	-	-
2.13b	ENST00000368654	13b	ENSE00001144087	chr10:129907687-129900843	6845	KI67_HUMAN	806-3087	2282	0	-	-
2.14a	ENST00000368654	14a	ENSE00001144079	chr10:129899965-129899522	444	KI67_HUMAN	3088-3235	148	0	-	-
2.15	ENST00000368654	15	ENSE00001385972	chr10:129897519-129894923	2597	KI67_HUMAN	3236-3256	21	0	-	-

NMR Structure

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:98
 aligned with KI67_HUMAN | P46013 from UniProtKB/Swiss-Prot  Length:3256

    Alignment length:98
                                    12        22        32        42        52        62        72        82        92        
           KI67_HUMAN     3 PTRRLVTIKRSGVDGPHFPLSLSTCLFGRGIECDIRIQLPVVSKQHCKIEIHEQEAILHNFSSTNPTQVNGSVIDEPVRLKHGDVITIIDRSFRYENE 100
               SCOP domains d2affa_ A: Antigen ki-67                                                                           SCOP domains
               CATH domains 2affA00 A:3-100  [code=2.60.200.20, no name defined]                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....eeeeee....eeeee......eee.........eeeee....eeeee.......ee..ee....eee....eeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------FHA_DOMAIN  PDB: A:27-76 UniProt: 27-76           ------------------------ PROSITE
           Transcript 2 (1) Exon 2.2a  PDB: A:3-31       --------------------------Exon 2.4  PDB: A:58-96 UniProt: 58-96  ---- Transcript 2 (1)
           Transcript 2 (2) ----------------------------Exon 2.3  PDB: A:31-57     --------------------------------------2.5   Transcript 2 (2)
                 2aff A   3 PTRRLVTIKRSGVDGPHFPLSLSTCLFGRGIECDIRIQLPVVSKQHCKIEIHEQEAILHNFSSTNPTQVNGSVIDEPVRLKHGDVITIIDRSFRYENE 100
                                    12        22        32        42        52        62        72        82        92

Chain B from PDB  Type:PROTEIN  Length:40
 aligned with MK67I_HUMAN | Q9BYG3 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:40
                                   237       247       257       267
          MK67I_HUMAN   228 VDSQGPTPVCTPTFLERRKSQVAELNDDDKDDEIVFKQPI 267
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
               Transcript 1 1.7 Exon 1.8f  PDB: B:232-267            Transcript 1
                 2aff B 228 VDsQGPtPVCtPTFLERRKSQVAELNDDDKDDEIVFKQPI 267
                              |   |237|      247       257       267
                            230-SEP   |                             
                                234-TPO                             
                                    238-TPO

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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SMAD/FHA domain (62)

Superfamily: SMAD/FHA domain (62)

Family: FHA domain (36)

Protein domain: Antigen ki-67 (2)

Human (Homo sapiens) [TaxId: 9606] (2)

d2affa_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Tumour Suppressor Smad4 (52)

Homologous Superfamily: [code=2.60.200.20, no name defined] (26)

Human (Homo sapiens) (5)

2affA00

A:3-100

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

NMR Structure(hide GO term definitions)

Chain A (KI67_HUMAN | P46013)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0031100	animal organ regeneration	The regrowth of a lost or destroyed animal organ.
	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:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0034605	cellular response to heat	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:1990705	cholangiocyte proliferation	The multiplication or reproduction of cholangiocytes, resulting in the expansion of the cholangiocyte population. A cholangiocyte is an epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water.
	GO:0072574	hepatocyte proliferation	The multiplication or reproduction of hepatocytes, resulting in the expansion of a cell population. Hepatocytes form the main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules.
	GO:0030212	hyaluronan metabolic process	The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
	GO:0014070	response to organic cyclic compound	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 an organic cyclic compound stimulus.
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: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:0000793	condensed chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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 B (MK67I_HUMAN | Q9BYG3)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0010923	negative regulation of phosphatase activity	Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
	GO:0016072	rRNA metabolic process	The chemical reactions and pathways involving rRNA, ribosomal RNA, a structural constituent of ribosomes.
	GO:0009303	rRNA transcription	The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
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:0000794	condensed nuclear chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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.

NMR Structure
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	KI67_HUMAN \| P46013	:	1r21 5j28

1r21	THE SOLUTION STRUCTURE OF KI67FHA IN A FREE FORM

Description

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