4AWL - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   THE NF-Y TRANSCRIPTION FACTOR IS STRUCTURALLY AND FUNCTIONALLY A SEQUENCE SPECIFIC HISTONE

Authors :   M. Nardini, N. Gnesutta, G. Donati, R. Gatta, C. Forni, A. Fossati, C. Vo D. Moras, C. Romier, R. Mantovani, M. Bolognesi

Date :   04 Jun 12 (Deposition) - 30 Jan 13 (Release) - 30 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.08

Chains :   Asym./Biol. Unit : A,B,C,I,J

Keywords :   Transcription-Dna Complex, Nf-Y, Dna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Nardini, N. Gnesutta, G. Donati, R. Gatta, C. Forni, A. Fossati, C. Vonrhein, D. Moras, C. Romier, M. Bolognesi, R. Mantovani
Sequence-Specific Transcription Factor Nf-Y Displays Histone-Like Dna Binding And H2B-Like Ubiquitination.
Cell(Cambridge, Mass. ) V. 152 132 2013
PubMed-ID: 23332751 | Reference-DOI: 10.1016/J.CELL.2012.11.047

Molecule 1 - NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT ALPHA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 233-303
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CCAAT BOX DNA-BINDING PROTEIN SUBUNIT A, CAAT BOX DNA- BINDING PROTEIN SUBUNIT A, NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT A, NF-YA

Molecule 2 - NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 51-143
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	FRAGMENT NUMBERING 49-141 IS THE NUMBERING DEFINED IN THE LITERATURE
	Synonym	:	CCAAT BOX DNA-BINDING PROTEIN SUBUNIT B, CAAT BOX DNA- BINDING PROTEIN SUBUNIT B, NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B, NF-YB

Molecule 3 - NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 27-120
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CAAT BOX DNA-BINDING PROTEIN SUBUNIT C, CAAT BOX DNA- BINDING PROTEIN SUBUNIT C, NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C, NF-YC, TRANSACTIVATOR HSM-1/2

Molecule 4 - HSP70 PROMOTER FRAGMENT
	Chains	:	I
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

Molecule 5 - HSP70 PROMOTER FRAGMENT
	Chains	:	J
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	B	C	I	J

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4AWL)

(no "Site" information available for 4AWL)

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

(no "Cis Peptide Bond" information available for 4AWL)

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NFYB_HAP3	PS00685	NF-YB/HAP3 subunit signature.	NFYB_HUMAN	89-105	1	B:87-103
2	NFYA_HAP2_2	PS51152	NF-YA/HAP2 family profile.	NFYA_HUMAN	261-321	1	A:233-292
3	NFYA_HAP2_1	PS00686	NF-YA/HAP2 subunit signature.	NFYA_HUMAN	266-286	1	A:237-257

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000240055	1	ENSE00001193640	chr12:104532040-104531919	122	NFYB_HUMAN	-	0	0	-	-
1.2	ENST00000240055	2	ENSE00001193633	chr12:104529310-104529226	85	NFYB_HUMAN	1-2	2	0	-	-
1.3	ENST00000240055	3	ENSE00000922958	chr12:104522295-104522202	94	NFYB_HUMAN	3-34	32	0	-	-
1.4	ENST00000240055	4	ENSE00000922957	chr12:104520022-104519892	131	NFYB_HUMAN	34-77	44	1	B:50-75	26
1.5	ENST00000240055	5	ENSE00000937932	chr12:104517201-104517004	198	NFYB_HUMAN	78-143	66	1	B:76-141	66
1.6	ENST00000240055	6	ENSE00000937933	chr12:104515099-104515018	82	NFYB_HUMAN	144-171	28	0	-	-
1.7	ENST00000240055	7	ENSE00001104711	chr12:104514257-104514178	80	NFYB_HUMAN	171-197	27	0	-	-
1.8	ENST00000240055	8	ENSE00001104713	chr12:104513547-104510858	2690	NFYB_HUMAN	198-207	10	0	-	-

2.13c	ENST00000308733	13c	ENSE00001428593	chr1:41204510-41204620	111	NFYC_HUMAN	1-35	35	0	-	-
2.14b	ENST00000308733	14b	ENSE00001643321	chr1:41213206-41213277	72	NFYC_HUMAN	36-59	24	1	C:40-59	20
2.15b	ENST00000308733	15b	ENSE00001609714	chr1:41215245-41215358	114	NFYC_HUMAN	60-97	38	1	C:60-97	38
2.16b	ENST00000308733	16b	ENSE00002187131	chr1:41218823-41218918	96	NFYC_HUMAN	98-129	32	1	C:98-119	22
2.17b	ENST00000308733	17b	ENSE00001145012	chr1:41223793-41223966	174	NFYC_HUMAN	130-187	58	0	-	-
2.18b	ENST00000308733	18b	ENSE00000870110	chr1:41228560-41228718	159	NFYC_HUMAN	188-240	53	0	-	-
2.21d	ENST00000308733	21d	ENSE00001662239	chr1:41232268-41232375	108	NFYC_HUMAN	241-276	36	0	-	-
2.21h	ENST00000308733	21h	ENSE00001080407	chr1:41232590-41232646	57	NFYC_HUMAN	277-295	19	0	-	-
2.22c	ENST00000308733	22c	ENSE00001683645	chr1:41235028-41235087	60	NFYC_HUMAN	296-315	20	0	-	-
2.23d	ENST00000308733	23d	ENSE00001433396	chr1:41236069-41237275	1207	NFYC_HUMAN	316-458	143	0	-	-

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:62
 aligned with NFYA_HUMAN | P23511 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:62
                                   270       280       290       300       310       320  
           NFYA_HUMAN   261 EEEPLYVNAKQYHRILKRRQARAKLEAEGKIPKERRKYLHESRHRHAMARKRGEGGRFFSPK 322
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh.............hhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NFYA_HAP2_2  PDB: A:233-292 UniProt: 261-321                 - PROSITE (1)
                PROSITE (2) -----NFYA_HAP2_1          ------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------- Transcript
                 4awl A 232 MEEPLYVNAKQYHRILKRRQARAKLEAEGKIPKERRKYLHESRHRHAMARKRGEGGRFFSPK 293
                                   241       251       261       271       281       291

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with NFYB_HUMAN | P25208 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:92
                                    61        71        81        91       101       111       121       131       141  
           NFYB_HUMAN    52 FREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQKFRE 143
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhh......ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhhhhhhh......hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------NFYB_HAP3        -------------------------------------- PROSITE
               Transcript 1 Exon 1.4  PDB: B:50-75    Exon 1.5  PDB: B:76-141 UniProt: 78-143                            Transcript 1
                 4awl B  50 FREQDIYLPIANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQKFRE 141
                                    59        69        79        89        99       109       119       129       139

Chain C from PDB  Type:PROTEIN  Length:80
 aligned with NFYC_HUMAN | Q13952 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:80
                                    49        59        69        79        89        99       109       119
           NFYC_HUMAN    40 VQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVP 119
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh.......ee..hhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.14b          Exon 2.15b  PDB: C:60-97              Exon 2.16b             Transcript 2
                 4awl C  40 VQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVP 119
                                    49        59        69        79        89        99       109       119

Chain I from PDB  Type:DNA  Length:25
                                                         
                 4awl I   1 TTCTGAGCCAATCACCGAGCTCGAT  25
                                    10        20

Chain J from PDB  Type:DNA  Length:25
                                                         
                 4awl J -25 ATCGAGCTCGGTGATTGGCTCAGAA  -1
                                   -16        -6

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 4AWL)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NFYA_HUMAN | P23511)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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:0001221	transcription cofactor binding	Interacting selectively and non-covalently with a transcription cofactor, any protein involved in regulation of transcription via protein-protein interactions with transcription factors and other transcription regulatory proteins. Cofactors do not bind DNA directly, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
	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:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	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.
biological process
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	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.
cellular component
	GO:0016602	CCAAT-binding factor complex	A heteromeric transcription factor complex that binds to the CCAAT-box upstream of promoters; functions as both an activator and a repressor, depending on its interacting cofactors. Typically trimeric consisting of NFYA, NFYB and NFYC subunits. In Saccharomyces, it activates the transcription of genes in response to growth in a nonfermentable carbon source and consists of four known subunits: HAP2, HAP3, HAP4 and HAP5.
	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:0032993	protein-DNA complex	A macromolecular complex containing both protein and DNA molecules.

Chain B (NFYB_HUMAN | P25208)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0032403	protein complex binding	Interacting selectively and non-covalently with any 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.
	GO:0070491	repressing transcription factor binding	Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	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.
biological process
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0016602	CCAAT-binding factor complex	A heteromeric transcription factor complex that binds to the CCAAT-box upstream of promoters; functions as both an activator and a repressor, depending on its interacting cofactors. Typically trimeric consisting of NFYA, NFYB and NFYC subunits. In Saccharomyces, it activates the transcription of genes in response to growth in a nonfermentable carbon source and consists of four known subunits: HAP2, HAP3, HAP4 and HAP5.
	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:0032993	protein-DNA complex	A macromolecular complex containing both protein and DNA molecules.

Chain C (NFYC_HUMAN | Q13952)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	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.
	GO:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	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:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	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:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
	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:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	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.
cellular component
	GO:0016602	CCAAT-binding factor complex	A heteromeric transcription factor complex that binds to the CCAAT-box upstream of promoters; functions as both an activator and a repressor, depending on its interacting cofactors. Typically trimeric consisting of NFYA, NFYB and NFYC subunits. In Saccharomyces, it activates the transcription of genes in response to growth in a nonfermentable carbon source and consists of four known subunits: HAP2, HAP3, HAP4 and HAP5.
	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:0032993	protein-DNA complex	A macromolecular complex containing both protein and DNA molecules.

Asymmetric/Biological Unit
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	4awl
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	NFYB_HUMAN \| P25208	:	1n1j 4csr
	NFYC_HUMAN \| Q13952	:	1n1j 4csr

1n1j	CRYSTAL STRUCTURE OF THE NF-YB/NF-YC HISTONE PAIR

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