3O10 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE HEPN DOMAIN FROM HUMAN SACSIN

Authors :   G. Kozlov, K. Gehring

Date :   20 Jul 10 (Deposition) - 30 Mar 11 (Release) - 30 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   All-Helical Domain, Homodimerization, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Kozlov, A. Y. Denisov, M. Girard, M. J. Dicaire, J. Hamlin, P. S. Mcpherson, B. Brais, K. Gehring
Structural Basis Of Defects In The Sacsin Hepn Domain Responsible For Autosomal Recessive Spastic Ataxia Of Charlevoix-Saguenay (Arsacs).
J. Biol. Chem. V. 286 20407 2011
PubMed-ID: 21507954 | Reference-DOI: 10.1074/JBC.M111.232884

Molecule 1 - SACSIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T-1
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	HEPN DOMAIN RESIDUES 4440-4579
	Gene	:	SACS, KIAA0730
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DNAJ HOMOLOG SUBFAMILY C MEMBER 29, DNAJC29

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 15)

No.	Name	Count	Type	Full Name
1	MLI	3	Ligand/Ion	MALONATE ION
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	MLI	2	Ligand/Ion	MALONATE ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	MLI	1	Ligand/Ion	MALONATE ION
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:13 , HOH A:124 , TYR A:4478 , LYS A:4482 , SER A:4533 , ARG A:4537 , ARG B:4537 , TYR B:4538	BINDING SITE FOR RESIDUE MLI A 1
2	AC2	SOFTWARE	ARG A:4537 , TYR A:4538 , HOH B:18 , HOH B:43 , HOH B:87 , HOH B:101 , TYR B:4478 , LYS B:4482 , SER B:4533	BINDING SITE FOR RESIDUE MLI B 1
3	AC3	SOFTWARE	HOH B:10 , SER B:4459 , ARG B:4462 , HOH D:7 , HOH D:42 , HOH D:59 , ARG D:4448 , ARG D:4452	BINDING SITE FOR RESIDUE MLI D 1

(no "SS Bond" information available for 3O10)

Asymmetric Unit

No.	Residues
1	Phe A:4544	-	Pro A:4545
2	Phe B:4544	-	Pro B:4545
3	Phe C:4544	-	Pro C:4545
4	Phe D:4544	-	Pro D:4545

Asymmetric Unit (2, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_064825	K	4508	T	SACS_HUMAN	Disease (SACS)	---	A/B/C/D	K	4508	T
2	UniProt	VAR_064826	N	4549	D	SACS_HUMAN	Disease (SACS)	---	A/B/C/D	N	4549	D

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

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_064825	K	4508	T	SACS_HUMAN	Disease (SACS)	---	A/B	K	4508	T
2	UniProt	VAR_064826	N	4549	D	SACS_HUMAN	Disease (SACS)	---	A/B	N	4549	D

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

Biological Unit 2 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_064825	K	4508	T	SACS_HUMAN	Disease (SACS)	---	C/D	K	4508	T
2	UniProt	VAR_064826	N	4549	D	SACS_HUMAN	Disease (SACS)	---	C/D	N	4549	D

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEPN	PS50910	HEPN domain profile.	SACS_HUMAN	4451-4567	4	A:4451-4567 B:4451-4567 C:4451-4567 D:4451-4567

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEPN	PS50910	HEPN domain profile.	SACS_HUMAN	4451-4567	2	A:4451-4567 B:4451-4567 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEPN	PS50910	HEPN domain profile.	SACS_HUMAN	4451-4567	2	- - C:4451-4567 D:4451-4567

Asymmetric Unit (1, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000382292	2b	ENSE00001548892	chr13:23985652-23985359	294	SACS_HUMAN	1-7	7	0	-	-
1.4	ENST00000382292	4	ENSE00001762476	chr13:23949408-23949258	151	SACS_HUMAN	7-57	51	0	-	-
1.5	ENST00000382292	5	ENSE00001749661	chr13:23945304-23945217	88	SACS_HUMAN	58-87	30	0	-	-
1.6a	ENST00000382292	6a	ENSE00001794623	chr13:23942626-23942541	86	SACS_HUMAN	87-115	29	0	-	-
1.7	ENST00000382292	7	ENSE00001738413	chr13:23939416-23939305	112	SACS_HUMAN	116-153	38	0	-	-
1.8	ENST00000382292	8	ENSE00001764306	chr13:23932620-23932474	147	SACS_HUMAN	153-202	50	0	-	-
1.9a	ENST00000382292	9a	ENSE00001739205	chr13:23930146-23928658	1489	SACS_HUMAN	202-698	497	0	-	-
1.10a	ENST00000382292	10a	ENSE00001745943	chr13:23928015-23927924	92	SACS_HUMAN	698-729	32	0	-	-
1.11b	ENST00000382292	11b	ENSE00001731339	chr13:23915829-23902965	12865	SACS_HUMAN	729-4579	3851	4	A:4439-4577 B:4439-4577 C:4442-4577 D:4440-4576	139 139 136 137

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:139
 aligned with SACS_HUMAN | Q9NZJ4 from UniProtKB/Swiss-Prot  Length:4579

    Alignment length:139
                                  4448      4458      4468      4478      4488      4498      4508      4518      4528      4538      4548      4558      4568         
          SACS_HUMAN   4439 KSVGNPVEARRWLRQARANFSAARNDLHKNANEWVCFKCYLSTKLALIAADYAVRGKSDKDVKPTALAQKIEEYSQQLEGLTNDVHTLEAYGVDSLKTRYPDLLPFPQIPNDRFTSEVAMRVMECTACIIIKLENFMQQ 4577
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------T----------------------------------------D---------------------------- SAPs(SNPs)
                    PROSITE ------------HEPN  PDB: A:4451-4567 UniProt: 4451-4567                                                                            ---------- PROSITE
               Transcript 1 Exon 1.11b  PDB: A:4439-4577 UniProt: 729-4579 [INCOMPLETE]                                                                                 Transcript 1
                3o10 A 4439 GSVGNPVEARRWLRQARANFSAARNDLHKNANEWVCFKCYLSTKLALIAADYAVRGKSDKDVKPTALAQKIEEYSQQLEGLTNDVHTLEAYGVDSLKTRYPDLLPFPQIPNDRFTSEVAmRVmECTACIIIKLENFmQQ 4577
                                  4448      4458      4468      4478      4488      4498      4508      4518      4528      4538      4548      4558  |   4568      |  
                                                                                                                                                4558-MSE         4575-MSE
                                                                                                                                                   4561-MSE

Chain B from PDB  Type:PROTEIN  Length:139
 aligned with SACS_HUMAN | Q9NZJ4 from UniProtKB/Swiss-Prot  Length:4579

    Alignment length:139
                                  4448      4458      4468      4478      4488      4498      4508      4518      4528      4538      4548      4558      4568         
          SACS_HUMAN   4439 KSVGNPVEARRWLRQARANFSAARNDLHKNANEWVCFKCYLSTKLALIAADYAVRGKSDKDVKPTALAQKIEEYSQQLEGLTNDVHTLEAYGVDSLKTRYPDLLPFPQIPNDRFTSEVAMRVMECTACIIIKLENFMQQ 4577
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------T----------------------------------------D---------------------------- SAPs(SNPs)
                    PROSITE ------------HEPN  PDB: B:4451-4567 UniProt: 4451-4567                                                                            ---------- PROSITE
               Transcript 1 Exon 1.11b  PDB: B:4439-4577 UniProt: 729-4579 [INCOMPLETE]                                                                                 Transcript 1
                3o10 B 4439 GSVGNPVEARRWLRQARANFSAARNDLHKNANEWVCFKCYLSTKLALIAADYAVRGKSDKDVKPTALAQKIEEYSQQLEGLTNDVHTLEAYGVDSLKTRYPDLLPFPQIPNDRFTSEVAmRVmECTACIIIKLENFmQQ 4577
                                  4448      4458      4468      4478      4488      4498      4508      4518      4528      4538      4548      4558  |   4568      |  
                                                                                                                                                4558-MSE         4575-MSE
                                                                                                                                                   4561-MSE

Chain C from PDB  Type:PROTEIN  Length:136
 aligned with SACS_HUMAN | Q9NZJ4 from UniProtKB/Swiss-Prot  Length:4579

    Alignment length:136
                                  4451      4461      4471      4481      4491      4501      4511      4521      4531      4541      4551      4561      4571      
          SACS_HUMAN   4442 GNPVEARRWLRQARANFSAARNDLHKNANEWVCFKCYLSTKLALIAADYAVRGKSDKDVKPTALAQKIEEYSQQLEGLTNDVHTLEAYGVDSLKTRYPDLLPFPQIPNDRFTSEVAMRVMECTACIIIKLENFMQQ 4577
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------T----------------------------------------D---------------------------- SAPs(SNPs)
                    PROSITE ---------HEPN  PDB: C:4451-4567 UniProt: 4451-4567                                                                            ---------- PROSITE
               Transcript 1 Exon 1.11b  PDB: C:4442-4577 UniProt: 729-4579 [INCOMPLETE]                                                                              Transcript 1
                3o10 C 4442 GNPVEARRWLRQARANFSAARNDLHKNANEWVCFKCYLSTKLALIAADYAVRGKSDKDVKPTALAQKIEEYSQQLEGLTNDVHTLEAYGVDSLKTRYPDLLPFPQIPNDRFTSEVAmRVmECTACIIIKLENFmQQ 4577
                                  4451      4461      4471      4481      4491      4501      4511      4521      4531      4541      4551      4561      4571   |  
                                                                                                                                             4558-MSE         4575-MSE
                                                                                                                                                4561-MSE

Chain D from PDB  Type:PROTEIN  Length:137
 aligned with SACS_HUMAN | Q9NZJ4 from UniProtKB/Swiss-Prot  Length:4579

    Alignment length:137
                                  4449      4459      4469      4479      4489      4499      4509      4519      4529      4539      4549      4559      4569       
          SACS_HUMAN   4440 SVGNPVEARRWLRQARANFSAARNDLHKNANEWVCFKCYLSTKLALIAADYAVRGKSDKDVKPTALAQKIEEYSQQLEGLTNDVHTLEAYGVDSLKTRYPDLLPFPQIPNDRFTSEVAMRVMECTACIIIKLENFMQ 4576
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------HEPN-3o10D01 D:4447-4574                                                                                                        -- Pfam domains (1)
           Pfam domains (2) -------HEPN-3o10D02 D:4447-4574                                                                                                        -- Pfam domains (2)
           Pfam domains (3) -------HEPN-3o10D03 D:4447-4574                                                                                                        -- Pfam domains (3)
           Pfam domains (4) -------HEPN-3o10D04 D:4447-4574                                                                                                        -- Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------T----------------------------------------D--------------------------- SAPs(SNPs)
                    PROSITE -----------HEPN  PDB: D:4451-4567 UniProt: 4451-4567                                                                            --------- PROSITE
               Transcript 1 Exon 1.11b  PDB: D:4440-4576 UniProt: 729-4579 [INCOMPLETE]                                                                               Transcript 1
                3o10 D 4440 SVGNPVEARRWLRQARANFSAARNDLHKNANEWVCFKCYLSTKLALIAADYAVRGKSDKDVKPTALAQKIEEYSQQLEGLTNDVHTLEAYGVDSLKTRYPDLLPFPQIPNDRFTSEVAmRVmECTACIIIKLENFmQ 4576
                                  4449      4459      4469      4479      4489      4499      4509      4519      4529      4539      4549      4559 |    4569     | 
                                                                                                                                               4558-MSE         4575-MSE
                                                                                                                                                  4561-MSE

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 3O10)

(no "CATH Domain" information available for 3O10)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: KNTase_C (11)

Family: HEPN (3)

Homo sapiens (Human) (1)

1a	HEPN-3o10D01	D:4447-4574
1b	HEPN-3o10D02	D:4447-4574
1c	HEPN-3o10D03	D:4447-4574
1d	HEPN-3o10D04	D:4447-4574

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SACS_HUMAN | Q9NZJ4)

molecular function
	GO:0030544	Hsp70 protein binding	Interacting selectively and non-covalently with Hsp70 proteins, any of a group of heat shock proteins around 70kDa in size.
	GO:0051087	chaperone binding	Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
	GO:0070628	proteasome binding	Interacting selectively and non-covalently with a proteasome, a large multisubunit protein complex that catalyzes protein degradation.
biological process
	GO:0090084	negative regulation of inclusion body assembly	Any process that decreases the rate, frequency, or extent of inclusion body assembly. Inclusion body assembly is the aggregation, arrangement and bonding together of a set of components to form an inclusion body.
	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.
cellular component
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0070852	cell body fiber	A neuron projection that is found in unipolar neurons and corresponds to the region between the cell body and the point at which the single projection branches.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	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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(no "Related Entries Specified in the PDB File" available for 3O10)

Description

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Ligands, Modified Residues, Ions (2, 15)

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SS Bonds (0, 0)

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