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NMR Structure - model 1 (Jmol Viewer)

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Title :   BRK DOMAIN FROM HUMAN CHD7

Authors :   M. D. Allen, T. L. Religa, S. M. V. Freund, M. Bycroft

Date :   14 May 07 (Deposition) - 22 May 07 (Release) - 19 Apr 17 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)
NMR Structure *: A  (1x)

Keywords :   Nucleotide-Binding, Chromatin Regulator, Charge Syndrome, Phosphorylation, Disease Mutation, Transcription Regulation, Chd7, Helicase, Hydrolase, Brk Domain, Atp-Binding, Dna-Binding, Transcription, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. D. Allen, T. L. Religa, S. M. V. Freund, M. Bycroft
Solution Structure Of The Brk Domains From Chd7
J. Mol. Biol. V. 371 1135 2007
PubMed-ID: 17603073 | Reference-DOI: 10.1016/J.JMB.2007.06.007

Molecule 1 - CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 7
	Chains	:	A
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	C41
	Expression System Taxid	:	562
	Expression System Vector Type	:	MODIFIED PRSETA
	Fragment	:	BRK DOMAIN, RESIDUES 1869-1953
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ATP- DEPENDENT HELICASE CHD7, CHD-7

		1
NMR Structure (20x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2V0F)

(no "Site" information available for 2V0F)

(no "SS Bond" information available for 2V0F)

(no "Cis Peptide Bond" information available for 2V0F)

NMR Structure (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068153	R	2653	Q	CHD7_HUMAN	Polymorphism	747082615	A	R	2653	Q
2	UniProt	VAR_068154	P	2683	S	CHD7_HUMAN	Unclassified (CHARGES)	201319489	A	P	2683	S
3	UniProt	VAR_068155	R	2702	C	CHD7_HUMAN	Unclassified (CHARGES)	---	A	R	2702	C

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

NMR Structure * (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068153	R	2653	Q	CHD7_HUMAN	Polymorphism	747082615	A	R	2653	Q
2	UniProt	VAR_068154	P	2683	S	CHD7_HUMAN	Unclassified (CHARGES)	201319489	A	P	2683	S
3	UniProt	VAR_068155	R	2702	C	CHD7_HUMAN	Unclassified (CHARGES)	---	A	R	2702	C

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

(no "PROSITE Motif" information available for 2V0F)

(no "Exon" information available for 2V0F)

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:87
 aligned with CHD7_HUMAN | Q9P2D1 from UniProtKB/Swiss-Prot  Length:2997

    Alignment length:87
                                  2638      2648      2658      2668      2678      2688      2698      2708       
          CHD7_HUMAN   2629 RCRNPNKLDINTLTGEERVPVVNKRNGKKMGGAMAPPMKDLPRWLEENPEFAVAPDWTDIVKQSGFVPESMFDRLLTGPVVRGEGAS 2715
               SCOP domains d2v0fa1 A:2629-2715 Chromodomain-helicase-DNA-binding protein 7, CHD7                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------BRK-2v0fA01 A:2640-2685                       ------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh.......eee.....ee.........hhhhhhhhh..eeehhhhhhhhhhhh..hhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------Q-----------------------------S------------------C------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                2v0f A 2629 GSRNPNKLDINTLTGEERVPVVNKRNGKKMGGAMAPPMKDLPRWLEENPEFAVAPDWTDIVKQSGFVPESMFDRLLTGPVVRGEGAS 2715
                                  2638      2648      2658      2668      2678      2688      2698      2708

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(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: GYF/BRK domain-like (9)

Superfamily: BRK domain-like (5)

Family: BRK domain-like (5)

Protein domain: Chromodomain-helicase-DNA-binding protein 7, CHD7 (3)

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

d2v0fa1

A:2629-2715

(no "CATH Domain" information available for 2V0F)

NMR Structure

Clans(

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Families(

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Organisms( (-)

)

Clan: no clan defined [family: BRK] (2)

Family: BRK (2)

Homo sapiens (Human) (2)

BRK-2v0fA01

A:2640-2685

NMR Structure(hide GO term definitions)

Chain A (CHD7_HUMAN | Q9P2D1)

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: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: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:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016817	hydrolase activity, acting on acid anhydrides	Catalysis of the hydrolysis of any acid anhydride.
	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:0030217	T cell differentiation	The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
	GO:0007512	adult heart development	The process whose specific outcome is the progression of the adult heart over time, from its formation to the mature structure.
	GO:0007628	adult walking behavior	The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.
	GO:0048844	artery morphogenesis	The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs.
	GO:0008015	blood circulation	The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products.
	GO:0001568	blood vessel development	The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.
	GO:0043010	camera-type eye development	The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
	GO:0007417	central nervous system development	The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
	GO:0050890	cognition	The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
	GO:0021545	cranial nerve development	The process whose specific outcome is the progression of the cranial nerves over time, from its formation to the mature structure. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions.
	GO:0042471	ear morphogenesis	The process in which the anatomical structures of the ear are generated and organized. The ear is the sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
	GO:0035116	embryonic hindlimb morphogenesis	The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal.
	GO:0060429	epithelium development	The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.
	GO:0060324	face development	The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head.
	GO:0030540	female genitalia development	The process whose specific outcome is the progression of the female genitalia over time, from formation to the mature structure.
	GO:0048806	genitalia development	The process whose specific outcome is the progression of the genitalia over time, from its formation to the mature structure.
	GO:0003007	heart morphogenesis	The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0001701	in utero embryonic development	The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
	GO:0042472	inner ear morphogenesis	The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
	GO:0060173	limb development	The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin.
	GO:0007626	locomotory behavior	The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
	GO:0043584	nose development	The process whose specific outcome is the progression of the nose over time, from its formation to the mature structure. The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity).
	GO:0042048	olfactory behavior	The behavior of an organism in response to an odor.
	GO:0021772	olfactory bulb development	The progression of the olfactory bulb over time from its initial formation until its mature state. The olfactory bulb coordinates neuronal signaling involved in the perception of smell. It receives input from the sensory neurons and outputs to the olfactory cortex.
	GO:0021553	olfactory nerve development	The process whose specific outcome is the progression of the olfactory nerve over time, from its formation to the mature structure. The olfactory nerve is a collection of sensory nerve rootlets that extend down from the olfactory bulb to the olfactory mucosa of the upper parts of the nasal cavity. This nerve conducts odor information to the brainstem.
	GO:0060021	palate development	The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
	GO:0040018	positive regulation of multicellular organism growth	Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0060123	regulation of growth hormone secretion	Any process that modulates the frequency, rate or extent of the regulated release of growth hormone from a cell.
	GO:0050767	regulation of neurogenesis	Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0060041	retina development in camera-type eye	The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
	GO:0048752	semicircular canal morphogenesis	The process in which the anatomical structures of the semicircular canals are generated and organized.
	GO:0007605	sensory perception of sound	The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
	GO:0001501	skeletal system development	The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	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.

NMR Structure
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	2v0f
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	3.6.1.-
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UniProtKB/Swiss-Prot
	CHD7_HUMAN \| Q9P2D1	:	2ckc 2v0e

2ckc	SOLUTION STRUCTURES OF THE BRK DOMAINS OF THE HUMAN CHROMO HELICASE DOMAIN 7 AND 8 , REVEALS STRUCTURAL SIMILARITY WITH GYF DOMAIN SUGGESTING A ROLE IN PROTEIN INTERACTION
2v0e	BRK DOMAIN FROM HUMAN CHD7

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