3NX0 - JenaLib

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Title :   HINGE-LOOP MUTATION CAN BE USED TO CONTROL 3D DOMAIN SWAPPING AND AMYLOIDOGENESIS OF HUMAN CYSTATIN C

Authors :   M. Orlikowska, E. Jankowska, R. Kolodziejczyk, M. Jaskolski, A. Szyma

Date :   12 Jul 10 (Deposition) - 01 Dec 10 (Release) - 02 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.04

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

Keywords :   Cysteine Protease Inhibitor, 3D Domain Swapping, Protein Engineering, Protein Oligomerization, Protein Aggregation, Amyloid, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Orlikowska, E. Jankowska, R. Kolodziejczyk, M. Jaskolski, A. Szymanska
Hinge-Loop Mutation Can Be Used To Control 3D Domain Swapping And Amyloidogenesis Of Human Cystatin C.
J. Struct. Biol. V. 173 406 2011
PubMed-ID: 21074623 | Reference-DOI: 10.1016/J.JSB.2010.11.009

Molecule 1 - CYSTATIN-C
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHD313
	Expression System Strain	:	C41(DE3)
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 27-146
	Gene	:	CST3
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYSTATIN-3, NEUROENDOCRINE BASIC POLYPEPTIDE, GAMMA-TRACE, POST-GAMMA-GLOBULIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:57 , ALA A:58 , GLY A:59 , TYR A:102 , HOH A:150 , HOH A:181	BINDING SITE FOR RESIDUE SO4 A 121
2	AC2	SOFTWARE	ASN B:57 , ALA B:58 , GLY B:59 , ASN B:61 , TYR B:102 , HOH B:190	BINDING SITE FOR RESIDUE SO4 B 121

Asymmetric Unit

No.	Residues
1	A:73	-	A:83
2	A:97	-	A:117
3	B:73	-	B:83
4	B:97	-	B:117

Asymmetric Unit

No.	Residues
1	Gly A:12	-	Pro A:13
2	Gly B:12	-	Pro B:13

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_002207	L	94	Q	CYTC_HUMAN	Disease (AMYL6)	28939068	A/B	L	68	Q

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_002207	L	94	Q	CYTC_HUMAN	Disease (AMYL6)	28939068	A	L	68	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
1	UniProt	VAR_002207	L	94	Q	CYTC_HUMAN	Disease (AMYL6)	28939068	B	L	68	Q

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYSTATIN	PS00287	Cysteine proteases inhibitors signature.	CYTC_HUMAN	80-93	2	A:54-67 B:54-67

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYSTATIN	PS00287	Cysteine proteases inhibitors signature.	CYTC_HUMAN	80-93	1	A:54-67 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYSTATIN	PS00287	Cysteine proteases inhibitors signature.	CYTC_HUMAN	80-93	1	- B:54-67

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2b	ENST00000398411	2b	ENSE00001533104	chr20:23618582-23618257	326	CYTC_HUMAN	1-81	81	2	A:12-55 B:12-55	44 44
1.3	ENST00000398411	3	ENSE00000660936	chr20:23616004-23615891	114	CYTC_HUMAN	82-119	38	2	A:56-93 B:56-93	38 38
1.4a	ENST00000398411	4a	ENSE00001533102	chr20:23614636-23614551	86	CYTC_HUMAN	120-146	27	2	A:94-120 B:94-120	27 27
1.5	ENST00000398411	5	ENSE00001533100	chr20:23610102-23608534	1569	CYTC_HUMAN	-	0	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:109
 aligned with CYTC_HUMAN | P01034 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:109
                                    47        57        67        77        87        97       107       117       127       137         
           CYTC_HUMAN    38 GPMDASVEEEGVRRALDFAVGEYNKASNDMYHSRALQVVRARKQIVAGVNYFLDVELGRTTCTKTQPNLDNCPFHDQPHLKRKAFCSFQIYAVPWQGTMTLSKSTCQDA 146
               SCOP domains d3nx0a_ A: Cystatin C                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....hhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeee...eeeeeeeeeeeeeee.............hhhhhh.eeeeeeeeeehhhheeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------Q---------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------CYSTATIN      ----------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2b  PDB: A:12-55 UniProt: 1-81       Exon 1.3  PDB: A:56-93 UniProt: 82-119Exon 1.4a  PDB: A:94-120    Transcript 1
                 3nx0 A  12 GPMDASVEEEGVRRALDFAVGEYNKASNDMYHSRALQVVRARKQINAGVNYFLDVELGRTTCTKTQPNLDNCPFHDQPHLKRKAFCSFQIYAVPWQGTMTLSKSTCQDA 120
                                    21        31        41        51        61        71        81        91       101       111

Chain B from PDB  Type:PROTEIN  Length:109
 aligned with CYTC_HUMAN | P01034 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:109
                                    47        57        67        77        87        97       107       117       127       137         
           CYTC_HUMAN    38 GPMDASVEEEGVRRALDFAVGEYNKASNDMYHSRALQVVRARKQIVAGVNYFLDVELGRTTCTKTQPNLDNCPFHDQPHLKRKAFCSFQIYAVPWQGTMTLSKSTCQDA 146
               SCOP domains d3nx0b_ B: Cystatin C                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Cystatin-3nx0B01 B:12-106                                                                      -------------- Pfam domains (1)
           Pfam domains (2) Cystatin-3nx0B02 B:12-106                                                                      -------------- Pfam domains (2)
         Sec.struct. author ..eee...hhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeee...eeeeeeeeeeeeeee.............hhhhhh.eeeeeeeeeehhhheeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------Q---------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------CYSTATIN      ----------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2b  PDB: B:12-55 UniProt: 1-81       Exon 1.3  PDB: B:56-93 UniProt: 82-119Exon 1.4a  PDB: B:94-120    Transcript 1
                 3nx0 B  12 GPMDASVEEEGVRRALDFAVGEYNKASNDMYHSRALQVVRARKQINAGVNYFLDVELGRTTCTKTQPNLDNCPFHDQPHLKRKAFCSFQIYAVPWQGTMTLSKSTCQDA 120
                                    21        31        41        51        61        71        81        91       101       111

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

Fold: Cystatin-like (403)

Superfamily: Cystatin/monellin (68)

Family: Cystatins (31)

Protein domain: Cystatin C (9)

Human (Homo sapiens) [TaxId: 9606] (9)

1a	d3nx0a_	A:
1b	d3nx0b_	B:

(no "CATH Domain" information available for 3NX0)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cystatin (20)

Family: Cystatin (15)

Homo sapiens (Human) (12)

1a	Cystatin-3nx0B01	B:12-106
1b	Cystatin-3nx0B02	B:12-106

Asymmetric Unit(hide GO term definitions)

Chain A,B (CYTC_HUMAN | P01034)

molecular function
	GO:0001540	amyloid-beta binding	Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
	GO:0004869	cysteine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0004866	endopeptidase inhibitor activity	Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0002020	protease binding	Interacting selectively and non-covalently with any protease or peptidase.
	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:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0060313	negative regulation of blood vessel remodeling	Any process that decreases the rate, frequency or extent of blood vessel remodeling, the reorganization or renovation of existing blood vessels.
	GO:0010711	negative regulation of collagen catabolic process	Any process that decreases the rate, frequency or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix.
	GO:0060311	negative regulation of elastin catabolic process	Any process that decreases the rate, frequency or extent of elastin catabolism, the chemical reactions and pathways resulting in the breakdown of elastin.
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010716	negative regulation of extracellular matrix disassembly	Any process that decreases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:0045861	negative regulation of proteolysis	Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
	GO:0034103	regulation of tissue remodeling	Any process that modulates the frequency, rate, or extent of tissue remodeling.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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Description

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