1LJM - 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)

Biological Unit 4 (Jmol Viewer)

Title :   DNA RECOGNITION IS MEDIATED BY CONFORMATIONAL TRANSITION AND BY DNA BENDING

Authors :   D. Bartfeld, L. Shimon, G. C. Couture, D. Rabinovich, F. Frolow, D. Levanon, Y. Groner, Z. Shakked

Date :   22 Apr 02 (Deposition) - 06 Nov 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (2x)
Biol. Unit 4: B  (2x)

Keywords :   Immunoglobulin Fold, Beta-Sandwich, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Bartfeld, L. Shimon, G. Couture, D. Rabinovich, F. Frolow, D. Levanon, Y. Groner, Z. Shakked
Dna Recognition By The Runx1 Transcription Factor Is Mediated By An Allosteric Transition In The Runt Domain And By Dna Bending.
Structure V. 10 1395
PubMed-ID: 12377125 | Reference-DOI: 10.1016/S0969-2126(02)00853-5
(for further references see the PDB file header)

Molecule 1 - RUNX1 TRANSCRIPTION FACTOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	RUNT-PV-8
	Expression System Strain	:	PHS2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PV/8+LAMBDAPL+RBS
	Fragment	:	RUNT DOMAIN
	Gene	:	HUMAN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RUNT-RELATED TRANSCRIPTION FACTOR 1, ACUTE MYELOID LEUKEMIA 1 PROTEIN, CORE-BINDING FACTOR, ALPHA 2 SUBUNIT

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (2x)	:	A	B
Biological Unit 4 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	CL	5	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR B:2154 , ASN B:2155	BINDING SITE FOR RESIDUE CL B 4001
2	AC2	SOFTWARE	GLN B:2158 , HOH B:3056	BINDING SITE FOR RESIDUE CL B 4002
3	AC3	SOFTWARE	ALA A:1115 , GLU A:1116 , GLY A:1138	BINDING SITE FOR RESIDUE CL A 4003
4	AC4	SOFTWARE	ASN B:2112 , ALA B:2115 , GLU B:2116 , GLY B:2138	BINDING SITE FOR RESIDUE CL B 4004
5	AC5	SOFTWARE	ARG B:2142 , THR B:2169 , VAL B:2170	BINDING SITE FOR RESIDUE CL B 4005

(no "SS Bond" information available for 1LJM)

Asymmetric Unit

No.	Residues
1	Asn A:1155	-	Pro A:1156
2	Asn B:2155	-	Pro B:2156

Asymmetric Unit (2, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012129	R	174	Q	RUNX1_HUMAN	Disease (FPDMM)	74315450	A	R	1174	Q
2	UniProt	VAR_012128	R	139	Q	RUNX1_HUMAN	Disease (FPDMM)	---	A B	R	1139 2139	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012129	R	174	Q	RUNX1_HUMAN	Disease (FPDMM)	74315450	A	R	1174	Q
2	UniProt	VAR_012128	R	139	Q	RUNX1_HUMAN	Disease (FPDMM)	---	A A	R	1139 2139	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
2	UniProt	VAR_012128	R	139	Q	RUNX1_HUMAN	Disease (FPDMM)	---	A B	R	1139 2139	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (2, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_012129	R	174	Q	RUNX1_HUMAN	Disease (FPDMM)	74315450	A	R	1174	Q
2	UniProt	VAR_012128	R	139	Q	RUNX1_HUMAN	Disease (FPDMM)	---	A A/B	R	1139 2139	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
2	UniProt	VAR_012128	R	139	Q	RUNX1_HUMAN	Disease (FPDMM)	---	A B	R	1139 2139	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1LJM)

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.18a	ENST00000344691	18a	ENSE00001380483	chr21:36260987-36259140	1848	RUNX1_HUMAN	1-90	90	2	A:1061-1090 B:2060-2090	30 31
1.19c	ENST00000344691	19c	ENSE00001660291	chr21:36253010-36252854	157	RUNX1_HUMAN	91-143	53	2	A:1091-1143 B:2091-2143	53 53
1.20a	ENST00000344691	20a	ENSE00002199204	chr21:36231875-36231771	105	RUNX1_HUMAN	143-178	36	2	A:1143-1174 B:2143-2173	32 31
1.22a	ENST00000344691	22a	ENSE00002198909	chr21:36206898-36206707	192	RUNX1_HUMAN	178-242	65	0	-	-
1.25	ENST00000344691	25	ENSE00002149931	chr21:36171759-36171598	162	RUNX1_HUMAN	242-296	55	0	-	-
1.26e	ENST00000344691	26e	ENSE00001623427	chr21:36164907-36160098	4810	RUNX1_HUMAN	296-453	158	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:114
 aligned with RUNX1_HUMAN | Q01196 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:114
                                    70        80        90       100       110       120       130       140       150       160       170    
         RUNX1_HUMAN     61 ELVRTDSPNFLCSVLPTHWRCNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRNATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPR  174
               SCOP domains d1ljma_ A: Acute myeloid leukemia 1 protein (AML1), RUNT domain                                                    SCOP domains
               CATH domains 1ljmA00 A:1061-1174  [code=2.60.40.720, no name defined]                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eeee....eee.........eeee........eeeeeee........ee..eee....eee....ee..........eeeeee.....eeee.....eee..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------Q SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.18a  PDB: A:1061-1090  Exon 1.19c  PDB: A:1091-1143 UniProt: 91-143         ------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------Exon 1.20a  PDB: A:1143-1174     Transcript 1 (2)
                1ljm A 1061 ELVRTDSPNFLCSVLPTHWRCNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRNATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPR 1174
                                  1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with RUNX1_HUMAN | Q01196 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:114
                                    69        79        89        99       109       119       129       139       149       159       169    
         RUNX1_HUMAN     60 GELVRTDSPNFLCSVLPTHWRCNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRNATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGP  173
               SCOP domains d1ljmb_ B: Acute myeloid leukemia 1 protein (AML1), RUNT domain                                                    SCOP domains
               CATH domains 1ljmB00 B:2060-2173  [code=2.60.40.720, no name defined]                                                           CATH domains
           Pfam domains (1) Runt-1ljmB01 B:2060-2173                                                                                           Pfam domains (1)
           Pfam domains (2) Runt-1ljmB02 B:2060-2173                                                                                           Pfam domains (2)
         Sec.struct. author ...ee.....eee.....eee.........eeee........eeeeeee............eee....eee................eeeeee.....eeee.....eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------Q---------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.18a  PDB: B:2060-2090   Exon 1.19c  PDB: B:2091-2143 UniProt: 91-143         ------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------Exon 1.20a  PDB: B:2143-2173    Transcript 1 (2)
                1ljm B 2060 GELVRTDSPNFLCSVLPTHWRCNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRNATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGP 2173
                                  2069      2079      2089      2099      2109      2119      2129      2139      2149      2159      2169

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f (364)

Superfamily: p53-like transcription factors (153)

Family: RUNT domain (12)

Protein domain: Acute myeloid leukemia 1 protein (AML1), RUNT domain (11)

Human (Homo sapiens) [TaxId: 9606] (5)

1a	d1ljma_	A:
1b	d1ljmb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.720, no name defined] (49)

Human (Homo sapiens) (29)

1a	1ljmA00	A:1061-1174
1b	1ljmB00	B:2060-2173

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P53-like (54)

Family: Runt (1)

Homo sapiens (Human) (1)

1a	Runt-1ljmB01	B:2060-2173
1b	Runt-1ljmB02	B:2060-2173

Asymmetric Unit(hide GO term definitions)

Chain A,B (RUNX1_HUMAN | Q01196)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0001047	core promoter binding	Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. 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: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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0000975	regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair.
	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:0001228	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region 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:0002062	chondrocyte differentiation	The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage.
	GO:0071425	hematopoietic stem cell proliferation	The expansion of a hematopoietic stem cell population by cell division. A hematopoietic stem cell is a stem cell from which all cells of the lymphoid and myeloid lineages develop.
	GO:0030097	hemopoiesis	The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
	GO:0030099	myeloid cell differentiation	The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
	GO:0030853	negative regulation of granulocyte differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of granulocyte differentiation.
	GO:0001503	ossification	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
	GO:0048935	peripheral nervous system neuron development	The process whose specific outcome is the progression of a neuron whose cell body is located in the peripheral nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron.
	GO:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0030854	positive regulation of granulocyte differentiation	Any process that activates or increases the frequency, rate or extent of granulocyte differentiation.
	GO:0032743	positive regulation of interleukin-2 production	Any process that activates or increases the frequency, rate, or extent of interleukin-2 production.
	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: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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	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.

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	1ljm
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	RUNX1_HUMAN \| Q01196	:	1cmo 1co1 1e50 1h9d

(no "Related Entries Specified in the PDB File" available for 1LJM)

Description

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Ligands, Modified Residues, Ions (1, 5)

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