3F02 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CLEAVED HUMAN NEUROSERPIN

Authors :   S. Ricagno, G. Sorrentino, S. Caccia, M. Bolognesi

Date :   24 Oct 08 (Deposition) - 26 May 09 (Release) - 16 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Neuroserpin, Serpin, Cleaved Form, Fenib, Human, Disease Mutation, Glycoprotein, Protease Inhibitor, Secreted, Serine Protease Inhibitor, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ricagno, S. Caccia, G. Sorrentino, G. Antonini, M. Bolognesi
Human Neuroserpin: Structure And Time-Dependent Inhibition
J. Mol. Biol. V. 388 109 2009
PubMed-ID: 19265707 | Reference-DOI: 10.1016/J.JMB.2009.02.056

Molecule 1 - NEUROSERPIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA (DE3) PLYS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 17-362
	Gene	:	SERPINI1, PI12
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CLEAVED NEURSERPIN BY TRYPSIN
	Synonym	:	SERPIN I1, PROTEASE INHIBITOR 12

Molecule 2 - NEUROSERPIN
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	ROSETTA (DE3) PLYS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 363-410
	Gene	:	SERPINI1, PI12
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CLEAVED NEURSERPIN BY TRYPSIN
	Synonym	:	SERPIN I1, PROTEASE INHIBITOR 12

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3F02)

(no "Site" information available for 3F02)

(no "SS Bond" information available for 3F02)

(no "Cis Peptide Bond" information available for 3F02)

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_008520	S	49	P	NEUS_HUMAN	Disease (FENIB)	121909051	A/B	S	49	P
2	UniProt	VAR_008521	S	52	R	NEUS_HUMAN	Disease (FENIB)	---	A/B	S	52	R

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_008520	S	49	P	NEUS_HUMAN	Disease (FENIB)	121909051	A	S	49	P
2	UniProt	VAR_008521	S	52	R	NEUS_HUMAN	Disease (FENIB)	---	A	S	52	R

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

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_008520	S	49	P	NEUS_HUMAN	Disease (FENIB)	121909051	B	S	49	P
2	UniProt	VAR_008521	S	52	R	NEUS_HUMAN	Disease (FENIB)	---	B	S	52	R

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	NEUS_HUMAN	370-380	2	C:370-380 D:370-380

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	NEUS_HUMAN	370-380	1	C:370-380 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SERPIN	PS00284	Serpins signature.	NEUS_HUMAN	370-380	1	- D:370-380

(no "Exon" information available for 3F02)

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:322
 aligned with NEUS_HUMAN | Q99574 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:339
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         
           NEUS_HUMAN    24 EAIADLSVNMYNRLRATGEDENILFSPLSIALAMGMMELGAQGSTQKEIRHSMGYDSLKNGEEFSFLKEFSNMVTAKESQYVMKIANSLFVQNGFHVNEEFLQMMKKYFNAAVNHVDFSQNVAVANYINKWVENNTNNLVKDLVSPRDFDAATYLALINAVYFKGNWKSQFRPENTRTFSFTKDDESEVQIPMMYQQGEFYYGEFSDGSNEAGGIYQVLEIPYEGDEISMMLVLSRQEVPLATLEPLVKAQLVEEWANSVKKQKVEVYLPRFTVEQEIDLKDVLKALGITEIFIKDANLTGLSDNKEIFLSKAIHKSFLEVNEEGSEAAAVSGMIAISR 362
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f02A01 A:24-192,A:295-362 Antithrombin, subunit I, domai    n 2                                                                                                         3f02A02 A:193-294 Alpha-1-antitrypsin, d   omain 1                                                    3f02A01 A:24-192,A:295-362 Antithrombin, subunit I, domain 2         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh...----hhhhhhhh.----------.eeeeeeeeeee.....hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhh.........hhhhh...eeeeeeeeeeeeee.....hhhhheeeeee.....eeeeeeeeeeeeeeeeeee...---..eeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhhhh.hhhhh.............eeeeeeeeeeeeee...eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------P--R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f02 A  24 EAIADLSVNMYNRLRATGEDENILFSPLSIALAMGMMELGAQGSTQKEIRHSMGYDS----EEFSFLKEF----------YVMKIANSLFVQNGFHVNEEFLQMMKKYFNAAVNHVDFSQNVAVANYINKWVENNTNNLVKDLVSPRDFDAATYLALINAVYFKGNWKSQFRPENTRTFSFTKDDESEVQIPMMYQQGEFYYGEFSDGS---GGIYQVLEIPYEGDEISMMLVLSRQEVPLATLEPLVKAQLVEEWANSVKKQKVEVYLPRFTVEQEIDLKDVLKALGITEIFIKDANLTGLSDNKEIFLSKAIHKSFLEVNEEGSEAAAVSGMIAISR 362
                                    33        43        53        63        73      |  - |      93         -|      113       123       133       143       153       163       173       183       193       203       213       223        |-  |    243       253       263       273       283       293       303       313       323       333       343       353         
                                                                                   80   85      93        104                                                                                                                             232 236

Chain B from PDB  Type:PROTEIN  Length:327
 aligned with NEUS_HUMAN | Q99574 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:339
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353         
           NEUS_HUMAN    24 EAIADLSVNMYNRLRATGEDENILFSPLSIALAMGMMELGAQGSTQKEIRHSMGYDSLKNGEEFSFLKEFSNMVTAKESQYVMKIANSLFVQNGFHVNEEFLQMMKKYFNAAVNHVDFSQNVAVANYINKWVENNTNNLVKDLVSPRDFDAATYLALINAVYFKGNWKSQFRPENTRTFSFTKDDESEVQIPMMYQQGEFYYGEFSDGSNEAGGIYQVLEIPYEGDEISMMLVLSRQEVPLATLEPLVKAQLVEEWANSVKKQKVEVYLPRFTVEQEIDLKDVLKALGITEIFIKDANLTGLSDNKEIFLSKAIHKSFLEVNEEGSEAAAVSGMIAISR 362
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f02B01 B:24-192,B:295-362 Antithrombin, subunit I, domain    2                                                                                                          3f02B02 B:193-294 Alpha-1-antitrypsin, do  main 1                                                     3f02B01 B:24-192,B:295-362 Antithrombin, subunit I, domain 2         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.....---hhhhhhhhh.-------...eeeeeeeeeee.....hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhh.........hhhhh...eeeeeeeeeeeeee.....hhhhheeeeee.....eeeeeeeeeeeeeeeeeee....--..eeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhhh..hhhhh.............eeeeeeeeeeeeee...eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------P--R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f02 B  24 EAIADLSVNMYNRLRATGEDENILFSPLSIALAMGMMELGAQGSTQKEIRHSMGYDSL---EEFSFLKEFS-------SQYVMKIANSLFVQNGFHVNEEFLQMMKKYFNAAVNHVDFSQNVAVANYINKWVENNTNNLVKDLVSPRDFDAATYLALINAVYFKGNWKSQFRPENTRTFSFTKDDESEVQIPMMYQQGEFYYGEFSDGSN--GGIYQVLEIPYEGDEISMMLVLSRQEVPLATLEPLVKAQLVEEWANSVKKQKVEVYLPRFTVEQEIDLKDVLKALGITEIFIKDANLTGLSDNKEIFLSKAIHKSFLEVNEEGSEAAAVSGMIAISR 362
                                    33        43        53        63        73       | - |      93|      103       113       123       133       143       153       163       173       183       193       203       213       223       233  |    243       253       263       273       283       293       303       313       323       333       343       353         
                                                                                    81  85       94     102                                                                                                                                233  |                                                                                                                              
                                                                                                                                                                                                                                              236

Chain C from PDB  Type:PROTEIN  Length:35
 aligned with NEUS_HUMAN | Q99574 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:35
                                   374       384       394     
           NEUS_HUMAN   365 VLYPQVIVDHPFFFLIRNRRTGTILFMGRVMHPET 399
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author ....eee....eeeeeee.....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE -----SERPIN     ------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 3f02 C 365 VLYPQVIVDHPFFFLIRNRRTGTILFMGRVMHPET 399
                                   374       384       394

Chain D from PDB  Type:PROTEIN  Length:37
 aligned with NEUS_HUMAN | Q99574 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:37
                                   373       383       393       
           NEUS_HUMAN   364 AVLYPQVIVDHPFFFLIRNRRTGTILFMGRVMHPETM 400
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author .....eee....eeeeeee.....eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------SERPIN     -------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 3f02 D 364 AVLYPQVIVDHPFFFLIRNRRTGTILFMGRVMHPETM 400
                                   373       383       393

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 3F02)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Antithrombin; Chain I, domain 2 (100)

Homologous Superfamily: Antithrombin, subunit I, domain 2 (100)

Human (Homo sapiens) (80)

1a	3f02B01	B:24-192,B:295-362
1b	3f02A01	A:24-192,A:295-362

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Alpha-1-antitrypsin; domain 1 (101)

Homologous Superfamily: Alpha-1-antitrypsin, domain 1 (101)

Human (Homo sapiens) (81)

2a	3f02B02	B:193-294
2b	3f02A02	A:193-294

(no "Pfam Domain" information available for 3F02)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (NEUS_HUMAN | Q99574)

molecular function
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	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: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: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:0007422	peripheral nervous system development	The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
	GO:0030155	regulation of cell adhesion	Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
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: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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
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Biological Units
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Access by PDB/NDB ID
	3f02
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	NEUS_HUMAN \| Q99574
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	604218
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	NEUS_HUMAN \| Q99574	:	3f5n 3fgq

3f5n	STRUCTURE OF FULL HUMAN NEUROSERPIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

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Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

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Exons (0, 0)

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