1JVK - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   THREE-DIMENSIONAL STRUCTURE OF AN IMMUNOGLOBULIN LIGHT CHAIN DIMER ACTING AS A LETHAL AMYLOID PRECURSOR

Authors :   P. C. Bourne, P. A. Ramsland, L. Shan, Z. -C. Fan, C. R. Dewitt, B. B. Shultz, S. S. Terzyan, A. B. Edmundson

Date :   30 Aug 01 (Deposition) - 03 May 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

Chains :   Asym./Biol. Unit : A,B

Keywords :   Immunoglobulin Light Chain Dimer, Amyloidogenic, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. C. Bourne, P. A. Ramsland, L. Shan, Z. C. Fan, C. R. Dewitt, B. B. Shultz, S. S. Terzyan, C. R. Moomaw, C. A. Slaughter, L. W. Guddat, A. B. Edmundson
Three-Dimensional Structure Of An Immunoglobulin Light-Chain Dimer With Amyloidogenic Properties.
Acta Crystallogr. , Sect. D V. 58 815 2002
PubMed-ID: 11976493 | Reference-DOI: 10.1107/S0907444902004183
(for further references see the PDB file header)

Molecule 1 - IMMUNOGLOBULIN LAMBDA LIGHT CHAIN
	Chains	:	A, B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IG A L; IMMUNOGLOBULIN LAMBDA-CHAIN; IG A1 BUR

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID

(no "Site" information available for 1JVK)

Asymmetric/Biological Unit

No.	Residues
1	A:22	-	A:90
2	A:139	-	A:198
3	B:22	-	B:90
4	B:139	-	B:198

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:145	-	Pro A:146
2	Tyr B:145	-	Pro B:146

(no "SAP(SNP)/Variant" information available for 1JVK)

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.	IGLC2_HUMAN	85-91	1	B:196-202

(no "Exon" information available for 1JVK)

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 A from PDB  Type:PROTEIN  Length:216
 aligned with Q6PJG0_HUMAN | Q6PJG0 from UniProtKB/TrEMBL  Length:235

    Alignment length:216
                                                                                                                             118                                                                                                                    
                                                                                                                           117 |                                                                                                                    
                                    29        39        49        59        69        79        89        99       109       118       128       138       148       158       168       178       188       198       208       218       228      
         Q6PJG0_HUMAN    20 QSALTQPASVSGSPGQSITISCTGTSTDVGSHSLVSWYQQHPGKAPKFLIFEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCCSYVGSGT-VVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC 234
               SCOP domains d1jvka1 A:1-112 Immunoglobulin light chain lambda variable domain, VL-lambda                                    d1jvka2 A:113-216 Immunoglobulin light chain lambda constant domain, CL-lambda                           SCOP domains
               CATH domains -1jvkA01 A:2-112 Immunoglobulins                                                                                1jvkA02 A:113-213 Immunoglobulins                                                                    --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeee....eeeeeee...........eeeeee......eeee.............eeeeee..eeeeeee..hhhhheeeeeee........ee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jvk A   1 xTALTQPASVSGSPGQSITVSCTGVSSIVGSYNLVSWYQQHPGKAPKLLTYEVNKRPSGVSDRFSGSKSGNSASLTISGLQAEDEADYYCSSYDGSSTSVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTAC 216
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
                            1-PCA

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with IGLC2_HUMAN | P0DOY2 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:215
                                                                                                                                           1                                                                                                       
                                     -         -         -         -         -         -         -         -         -         -         - |       9        19        29        39        49        59        69        79        89        99     
          IGLC2_HUMAN     - ---------------------------------------------------------------------------------------------------------------GQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE 104
               SCOP domains d1jvkb1 B:1-112 Immunoglobulin light chain lambda variable domain, VL-lambda                                    d1jvkb2 B:113-215 Immunoglobulin light chain lambda constant domain, CL-lambda                          SCOP domains
               CATH domains -1jvkB01 B:2-112 Immunoglobulins                                                                                1jvkB02 B:113-213 Immunoglobulins                                                                    -- CATH domains
           Pfam domains (1) --V-set-1jvkB03 B:3-110                                                                                       -------------C1-set-1jvkB01 B:124-211                                                                ---- Pfam domains (1)
           Pfam domains (2) --V-set-1jvkB04 B:3-110                                                                                       -------------C1-set-1jvkB02 B:124-211                                                                ---- Pfam domains (2)
         Sec.struct. author ........eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeee....ee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jvk B   1 xTALTQPASVSGSPGQSITVSCTGVSSIVGSYNLVSWYQQHPGKAPKLLTYEVNKRPSGVSDRFSGSKSGNSASLTISGLQAEDEADYYCSSYDGSSTSVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTA 215
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     
                            |                                                                                                                                                                                                                      
                            1-PCA

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with Q6PJG0_HUMAN | Q6PJG0 from UniProtKB/TrEMBL  Length:235

    Alignment length:215
                                                                                                                             118                                                                                                                   
                                                                                                                           117 |                                                                                                                   
                                    29        39        49        59        69        79        89        99       109       118       128       138       148       158       168       178       188       198       208       218       228     
         Q6PJG0_HUMAN    20 QSALTQPASVSGSPGQSITISCTGTSTDVGSHSLVSWYQQHPGKAPKFLIFEGSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCCSYVGSGT-VVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE 233
               SCOP domains d1jvkb1 B:1-112 Immunoglobulin light chain lambda variable domain, VL-lambda                                    d1jvkb2 B:113-215 Immunoglobulin light chain lambda constant domain, CL-lambda                          SCOP domains
               CATH domains -1jvkB01 B:2-112 Immunoglobulins                                                                                1jvkB02 B:113-213 Immunoglobulins                                                                    -- CATH domains
           Pfam domains (1) --V-set-1jvkB03 B:3-110                                                                                       -------------C1-set-1jvkB01 B:124-211                                                                ---- Pfam domains (1)
           Pfam domains (2) --V-set-1jvkB04 B:3-110                                                                                       -------------C1-set-1jvkB02 B:124-211                                                                ---- Pfam domains (2)
         Sec.struct. author ........eeee.....eeeeee...........eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeeee....eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeee....ee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jvk B   1 xTALTQPASVSGSPGQSITVSCTGVSSIVGSYNLVSWYQQHPGKAPKLLTYEVNKRPSGVSDRFSGSKSGNSASLTISGLQAEDEADYYCSSYDGSSTSVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTA 215
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     
                            1-PCA

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)

Human (Homo sapiens) (912)

1a	1jvkA01	A:2-112
1b	1jvkB01	B:2-112
1c	1jvkA02	A:113-213
1d	1jvkB02	B:113-213

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: C1-set (338)

Homo sapiens (Human) (218)

1a	C1-set-1jvkB01	B:124-211
1b	C1-set-1jvkB02	B:124-211

Family: V-set (144)

Homo sapiens (Human) (61)

2a	V-set-1jvkB03	B:3-110
2b	V-set-1jvkB04	B:3-110

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q6PJG0_HUMAN | Q6PJG0)

Chain B (IGLC2_HUMAN | P0DOY2)

Asymmetric/Biological Unit
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	Sites
(no "Sites" information available for 1jvk)

	Cis Peptide Bonds
		Tyr A:145 - Pro A:146	[ RasMol ]
		Tyr B:145 - Pro B:146	[ RasMol ]

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	1jvk
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UniProtKB/Swiss-Prot
	IGLC2_HUMAN \| P0DOY2	:	1lil 1zvo 2jb5 2jb6 3c2a 3tv3 3twc 3tyg 4eow 4lld 4llm 4llq 4llu 4llw 4lly 4o58 4o5i 5d9q 5iq7 5iq9
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	Q6PJG0_HUMAN \| Q6PJG0	:	1lgv 1lhz

(no "Related Entries Specified in the PDB File" available for 1JVK)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (2, 4)

CATH Domains (1, 4)

Pfam Domains (2, 4)

Gene Ontology (23, 23)

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