3UX9 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURAL INSIGHTS INTO A HUMAN ANTI-IFN ANTIBODY EXERTING THERAPEUTIC POTENTIAL FOR SYSTEMIC LUPUS ERYTHEMATOSUS

Authors :   S. Ouyang, L. X. Zhao, W. Liang, N. Shaw, Z. -J. Liu, M. -F. Liang

Date :   04 Dec 11 (Deposition) - 29 Feb 12 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Five Helices, Long Loop Connecting Helix, Hydrophobic Interactions, Cytokine-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ouyang, B. Gong, J. -Z. Li, L. -X. Zhao, W. Wu, F. -S. Zhang, L. Sun, S. -J. Wang, M. Pan, C. Li, W. Liang, N. Shaw, J. Zheng, G. -P. Zhao, Y. Wang, Z. -J. Liu, M. -F. Liang
Structural Insights Into A Human Anti-Ifn Antibody Exerting Therapeutic Potential For Systemic Lupus Erythematosus
J. Mol. Med. 2012
PubMed-ID: 22307521 | Reference-DOI: 10.1007/S00109-012-0866-3

Molecule 1 - INTERFERON ALPHA-1/13
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG 7
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	IFNA1, IFNA13
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	INTERFERON 1B, IFN-ALPHA-1/13, INTERFERON ALPHA-D, LEIF D

Molecule 2 - SCFV ANTIBODY
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		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)

(no "Ligand,Modified Residues,Ions" information available for 3UX9)

(no "Site" information available for 3UX9)

Asymmetric Unit

No.	Residues
1	A:29	-	A:139
2	B:24	-	B:91
3	B:156	-	B:230
4	C:29	-	C:139
5	D:24	-	D:91
6	D:156	-	D:230

(no "Cis Peptide Bond" information available for 3UX9)

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_013000	A	137	V	IFNA1_HUMAN	Polymorphism	2230050	A/C	A	114	V
2	UniProt	VAR_025173	A	163	G	IFNA1_HUMAN	Polymorphism	33965070	A/C	A	140	G

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_013000	A	137	V	IFNA1_HUMAN	Polymorphism	2230050	A	A	114	V
2	UniProt	VAR_025173	A	163	G	IFNA1_HUMAN	Polymorphism	33965070	A	A	140	G

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_013000	A	137	V	IFNA1_HUMAN	Polymorphism	2230050	C	A	114	V
2	UniProt	VAR_025173	A	163	G	IFNA1_HUMAN	Polymorphism	33965070	C	A	140	G

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTERFERON_A_B_D	PS00252	Interferon alpha, beta and delta family signature.	IFNA1_HUMAN	146-164	2	A:123-141 C:123-141

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTERFERON_A_B_D	PS00252	Interferon alpha, beta and delta family signature.	IFNA1_HUMAN	146-164	1	A:123-141 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTERFERON_A_B_D	PS00252	Interferon alpha, beta and delta family signature.	IFNA1_HUMAN	146-164	1	- C:123-141

(no "Exon" information available for 3UX9)

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:132
 aligned with IFNA1_HUMAN | P01562 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:148
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171        
          IFNA1_HUMAN    32 LDNRRTLMLLAQMSRISPSSCLMDRHDFGFPQEEFDGNQFQKAPAISVLHELIQQIFNLFTTKDSSAAWDEDLLDKFCTELYQQLNDLEACVMQEERVGETPLMNADSILAVKKYFRRITLYLTEKKYSPCAWEVVRAEIMRSLSLST 179
               SCOP domains d3ux9a_ A: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...hhhhh.........hhhhhh------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..----------.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------V-------------------------G---------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------INTERFERON_A_B_D   --------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ux9 A   9 LDNRRTLMLLAQMSRISPSSCLMDRHDFGFPQEEFD------APAISVLHELIQQIFNLFTTKDSSAAWDEDLLDKFCTELYQQLNDLEACVMQ----------NADSILAVKKYFRRITLYLTEKKYSPCAWEVVRAEIMRSLSLST 156
                                    18        28        38     |   -  |     58        68        78        88        98   |     -    |  118       128       138       148        
                                                              44     51                                                102        113

Chain B from PDB  Type:PROTEIN  Length:229
                                                                                                                                                                                                                                                                     
               SCOP domains d3ux9b1 B:4-111 automated matches                                                                           --d3ux9b2 B:136-254 automated matches                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee...........eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eeeee...eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee......eeee...eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ux9 B   4 IVLTQPPSVSGAPGQRVTISCSGSSSNIGSNYVSWYQQLPGTAPKLLIYDNNQRPSGVPDRFSGSKSGTSASLAITGLQSEDEADYYCQVRDNNENEWVFGGGTKLTVLEVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARYIDFGDHMDFWGQGTLVTVSSL 254
                                    13        23        33        43        53        63        73        83        93       103       135       145       155       165       175       185       195       205       215       225       235       245         
                                                                                                                                      112|                                                                                                                       
                                                                                                                                       135

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with IFNA1_HUMAN | P01562 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:148
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171        
          IFNA1_HUMAN    32 LDNRRTLMLLAQMSRISPSSCLMDRHDFGFPQEEFDGNQFQKAPAISVLHELIQQIFNLFTTKDSSAAWDEDLLDKFCTELYQQLNDLEACVMQEERVGETPLMNADSILAVKKYFRRITLYLTEKKYSPCAWEVVRAEIMRSLSLST 179
               SCOP domains d3ux9c_ C: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...hhhhh.........hhhhh--------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----------.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------V-------------------------G---------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------INTERFERON_A_B_D   --------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ux9 C   9 LDNRRTLMLLAQMSRISPSSCLMDRHDFGFPQEEF--------PAISVLHELIQQIFNLFTTKDSSAAWDEDLLDKFCTELYQQLNDLEACVM-----------NADSILAVKKYFRRITLYLTEKKYSPCAWEVVRAEIMRSLSLST 156
                                    18        28        38    |    -   |    58        68        78        88        98  |      -    |  118       128       138       148        
                                                             43       52                                              101         113

Chain D from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains d3ux9d1 D:4-111 automated matches                                                                           --d3ux9d2 D:136-255 automated matches                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee...........eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eeeee...eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee......eeee...eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ux9 D   4 IVLTQPPSVSGAPGQRVTISCSGSSSNIGSNYVSWYQQLPGTAPKLLIYDNNQRPSGVPDRFSGSKSGTSASLAITGLQSEDEADYYCQVRDNNENEWVFGGGTKLTVLEVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARYIDFGDHMDFWGQGTLVTVSSLE 255
                                    13        23        33        43        53        63        73        83        93       103       135       145       155       165       175       185       195       205       215       225       235       245       255
                                                                                                                                      112|                                                                                                                        
                                                                                                                                       135

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 alpha proteins (14657)

Fold: 4-helical cytokines (168)

Superfamily: 4-helical cytokines (168)

Family: Interferons/interleukin-10 (IL-10) (41)

Protein domain: automated matches (5)

Human (Homo sapiens) [TaxId: 9606] (4)

1a	d3ux9a_	A:
1b	d3ux9c_	C:

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Human (Homo sapiens) [TaxId: 9606] (448)

2a	d3ux9b1	B:4-111
2b	d3ux9b2	B:136-254
2c	d3ux9d1	D:4-111
2d	d3ux9d2	D:136-255

(no "CATH Domain" information available for 3UX9)

(no "Pfam Domain" information available for 3UX9)

Asymmetric Unit(hide GO term definitions)

Chain A,C (IFNA1_HUMAN | P01562)

molecular function
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0005126	cytokine receptor binding	Interacting selectively and non-covalently with a cytokine receptor.
	GO:0005132	type I interferon receptor binding	Interacting selectively and non-covalently with an interferon-type I receptor, a heterodimeric complex composed of an alpha subunit (IFNAR1) and a beta subunit (IFNAR2).
biological process
	GO:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	GO:0042100	B cell proliferation	The expansion of a B cell population by cell division. Follows B cell activation.
	GO:0002286	T cell activation involved in immune response	The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0019221	cytokine-mediated signaling pathway	A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	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:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0006959	humoral immune response	An immune response mediated through a body fluid.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0002323	natural killer cell activation involved in immune response	The change in morphology and behavior of a natural killer cell resulting from exposure a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response.
	GO:0033141	positive regulation of peptidyl-serine phosphorylation of STAT protein	Any process that activates or increases the frequency, rate or extent of the phosphorylation of a serine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
	GO:0060338	regulation of type I interferon-mediated signaling pathway	Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
	GO:0043330	response to exogenous dsRNA	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an exogenous double-stranded RNA stimulus.
	GO:0060337	type I interferon signaling pathway	A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
cellular component
	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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Biological Units
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	3ux9
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Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

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Exons (0, 0)

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