1JRH - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   COMPLEX (ANTIBODY/ANTIGEN)

Authors :   F. K. Winkler, S. Sogabe

Date :   23 Sep 97 (Deposition) - 25 Mar 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : H,I,L

Keywords :   Cytokine Receptor, Complex (Antibody/Antigen), Transmembrane, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Sogabe, F. Stuart, C. Henke, A. Bridges, G. Williams, A. Birch, F. K. Winkler, J. A. Robinson
Neutralizing Epitopes On The Extracellular Interferon Gamma Receptor (Ifngammar) Alpha-Chain Characterized By Homolog Scanning Mutagenesis And X-Ray Crystal Structure Of The A6 Fab-Ifngammar1-108 Complex.
J. Mol. Biol. V. 273 882 1997
PubMed-ID: 9367779 | Reference-DOI: 10.1006/JMBI.1997.1336
(for further references see the PDB file header)

Molecule 1 - ANTIBODY A6
	Chains	:	L
	Fragment	:	FAB FRAGMENT;PEPSIN DIGESTION OF INTACT ANTIBODY
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - ANTIBODY A6
	Chains	:	H
	Fragment	:	FAB FRAGMENT;PEPSIN DIGESTION OF INTACT ANTIBODY
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - INTERFERON-GAMMA RECEPTOR ALPHA CHAIN
	Chains	:	I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	N-TERMINAL DOMAIN
	Gene	:	CDNA
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	ESCHERICHIA COLI HIOREDOXIN GENE FUSION EXPRESSION SYSTEM, BOVINE ENTEROKINASE CLEAVAGE

		1	2	3
Asymmetric/Biological Unit	:	H	I	L

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1JRH)

(no "Site" information available for 1JRH)

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:92
2	H:142	-	H:208
3	I:60	-	I:68
4	L:23	-	L:88
5	L:134	-	L:194

Asymmetric/Biological Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Tyr L:140	-	Pro L:141
3	Phe H:148	-	Pro H:149
4	Glu H:150	-	Pro H:151

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_019281	V	61	I	INGR1_HUMAN	Polymorphism	17175322	I	V	44	I
2	UniProt	VAR_017577	C	77	Y	INGR1_HUMAN	Disease (IMD27A)	104893974	I	C	60	Y
3	UniProt	VAR_017578	I	87	T	INGR1_HUMAN	Disease (IMD27A)	104893973	I	I	70	T

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	L:193-198

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000367739	1a	ENSE00002147702	chr6:137540586-137540380	207	INGR1_HUMAN	1-29	29	1	I:11-12	2
1.3a	ENST00000367739	3a	ENSE00000764523	chr6:137528214-137528100	115	INGR1_HUMAN	29-67	39	1	I:12-50	39
1.4a	ENST00000367739	4a	ENSE00000764522	chr6:137527445-137527273	173	INGR1_HUMAN	67-125	59	1	I:50-105	56
1.5b	ENST00000367739	5b	ENSE00001719673	chr6:137525641-137525469	173	INGR1_HUMAN	125-182	58	0	-	-
1.6b	ENST00000367739	6b	ENSE00002146269	chr6:137524822-137524636	187	INGR1_HUMAN	183-245	63	0	-	-
1.7b	ENST00000367739	7b	ENSE00001707029	chr6:137522145-137522018	128	INGR1_HUMAN	245-287	43	0	-	-
1.8	ENST00000367739	8	ENSE00001597426	chr6:137519776-137518621	1156	INGR1_HUMAN	288-489	202	0	-	-

Asymmetric/Biological 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 H from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                     
               SCOP domains d1jrhh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                            d1jrhh2 H:114-221 Immunoglobulin heavy chain gamma constan SCOP domains
               CATH domains 1jrhH01 H:1-113 Immunoglobulins                                                                                           1jrhH02 H:114-217 Immunoglobulins                     ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee.........eeeeeee.........eeee....eee....hhheeeeee....eeeeee....hhh.eeeeeee................eee..................eee.......eee.............eee..eeeehhh.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1jrh H    1 AVKLQESGPGILKPSQTLSLTCSFSGFSLTTYGMGVGWIRQSSGKGLEWLAHIWWDDDKYYNPSLKSRLTISKDTSRNQVFLKITSVATADTATYYCARRAPFYGNHAMDYWGQGTTVTVSSAKTTPCLVYFPEPVTVTWNSGSSGVHTFPAVLQSDLYTLSSSVTCNVAHPASSTKVDK  221
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     ||101       111      |144|      157| || ||174     ||186     ||211       221
                                                             35A|                                             82A||               100A|||               118| ||    154||| || ||      180|      192|             
                                                              35B                                              82B|                100B||                142 ||     156|| || ||       183       208             
                                                                                                                82C                 100C|                  144|      157| || ||                                 
                                                                                                                                     100D                   147       161 || ||                                 
                                                                                                                                                                        163| ||                                 
                                                                                                                                                                         166 ||                                 
                                                                                                                                                                           168|                                 
                                                                                                                                                                            171

Chain I from PDB  Type:PROTEIN  Length:95
 aligned with INGR1_HUMAN | P15260 from UniProtKB/Swiss-Prot  Length:489

    Alignment length:95
                                    37        47        57        67        77        87        97       107       117     
         INGR1_HUMAN     28 SVPTPTNVTIESYNMNPIVYWEYQIMPQVPVFTVEVKNYGVKNSEWIDACINISHHYCNISDHVGDPSNSLWVRVKARVGQKESAYAKSEEFAVC  122
               SCOP domains d1jrhi_ I: Interferon-gamma receptor alpha chain                                                SCOP domains
               CATH domains 1jrhI00 I:11-105 Immunoglobulins                                                                CATH domains
               Pfam domains Tissue_fac-1jrhI01 I:11-96                                                            --------- Pfam domains
         Sec.struct. author ........eee......eee..........eeeeeeeee.......eeee......eee.hhh......eeeeeeeee................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------I---------------Y---------T----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.-------------------------------------Exon 1.4a  PDB: I:50-105 UniProt: 67-125 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -Exon 1.3a  PDB: I:12-50 UniProt: 29-67 ------------------------------------------------------- Transcript 1 (2)
                1jrh I   11 SVPTPTNVTIESYNMNPIVYWEYQIMPQVPVFTVEVKNYGVKNSEWIDACINISHHYCNISDHVGDPSNSLWVRVKARVGQKESAYAKSEEFAVS  105
                                    20        30        40        50        60        70        80        90       100

Chain L from PDB  Type:PROTEIN  Length:167
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:192
                                                                                                                             21                                                                                             
                                                                   1   5                           6           19           20|          22 25   26                                                                         
                                     -         -         -         1   |     -         -         - |      14    |    -       ||-         -|  |    27        37        47        57        67        77        87        97  
          IGKC_MOUSE      - ---------------------------------------ADAAP---------------------------TVSIFPPSSEQLTS------------GG-----------ASVV----CFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVK   99
               SCOP domains d1jrhl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                d1jrhl2 L:108-207 Immunogl          obulin light chain k               appa constant d SCOP domains
               CATH domains 1jrhL01 L:1-108 Immunoglobulins                                                                            1jrhL02 L:109-204 Immunog          lobulins                                       --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeee.............eeeeee..eeeeee....hhh..eeeeee...........eeee.......eee...eeee.......eee----------.................eee---------------..eee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1jrh L    1 SVEMTQSPSSFSVSLGDRVTITCKASEDIYNRLAWYQQKPGNAPRLLISGATSLETEVPSRFSGSGSGKDYTLSITSLQTEDVATYYCQQYWSTWTFGGGTKLEIKRADAAPTVSIFPCFLNNFYPKDINVK----------GVLNSWTDQDSKDSTYSMSS---------------TCEATHKTSTSPIVK  207
                                    10        20        30        40        50        60        70        80        90   ||  101       111       135       145 |       -  |    165       175 |       -       195       205  
                                                                                                                        94|                    119|          147        158                177             193              
                                                                                                                         96                     134

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

1a	1jrhL02	L:109-204
1b	1jrhH02	H:114-217
1c	1jrhH01	H:1-113
1d	1jrhI00	I:11-105
1e	1jrhL01	L:1-108

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: E-set (290)

Family: Tissue_fac (23)

Homo sapiens (Human) (23)

Tissue_fac-1jrhI01

I:11-96

Asymmetric/Biological Unit(hide GO term definitions)

Chain I (INGR1_HUMAN | P15260)

molecular function
	GO:0019955	cytokine binding	Interacting selectively and non-covalently with a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
	GO:0004906	interferon-gamma receptor activity	Combining with interferon-gamma (a type II interferon) and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
	GO:0042015	interleukin-20 binding	Interacting selectively and non-covalently with interleukin-20.
	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:0060333	interferon-gamma-mediated signaling pathway	A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
	GO:0060334	regulation of interferon-gamma-mediated signaling pathway	Any process that modulates the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor.
	GO:0009615	response to virus	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 a stimulus from a virus.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain L (IGKC_MOUSE | P01837)

molecular function
	GO:0003823	antigen binding	Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
	GO:0034987	immunoglobulin receptor binding	Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
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:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0006958	complement activation, classical pathway	Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006911	phagocytosis, engulfment	The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
	GO:0006910	phagocytosis, recognition	The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
	GO:0050871	positive regulation of B cell activation	Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0042571	immunoglobulin complex, circulating	An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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(no "Sites" information available for 1jrh)

	Cis Peptide Bonds
		Glu H:150 - Pro H:151	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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	1jrh
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	INGR1_HUMAN \| P15260
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(no "Related Entries Specified in the PDB File" available for 1JRH)

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (5, 5)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (3, 3)

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Exons (3, 3)

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