4F37 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE TETHERED N-TERMINUS OF ALZHEIMER'S DISEASE A PEPTIDE

Authors :   R. M. Nisbet, S. D. Nuttall, J. M. Caine, R. Rober, M. Hittaki, L. A. Pearc N. Davydova, C. L. Masters, J. N. Varghese, V. A. Streltsov

Date :   09 May 12 (Deposition) - 15 May 13 (Release) - 03 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.57

Chains :   Asym. Unit : A,B,F,H,K,L
Biol. Unit 1: A,H,L  (1x)
Biol. Unit 2: B,F,K  (1x)

Keywords :   Amyloid-Beta, Alzheimer'S Disease, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. M. Nisbet, S. D. Nuttall, R. Robert, J. M. Caine, O. Dolezal, M. Hattarki, L. A. Pearce, N. Davydova, C. L. Masters, J. N. Varghese, V. A. Streltsov
Structural Studies Of The Tethered N-Terminus Of The Alzheimer'S Disease Amyloid-Beta Peptide.
Proteins V. 81 1748 2013
PubMed-ID: 23609990 | Reference-DOI: 10.1002/PROT.24312

Molecule 1 - COLICIN-E7 IMMUNITY PROTEIN
	Chains	:	A, B
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	IMME7, MICROCIN-E7 IMMUNITY PROTEIN

Molecule 2 - IM7 IMMUNITY PROTEIN
	Cell	:	HYBRIDOMA
	Chains	:	F, H
	Engineered	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	IN VITRO

Molecule 3 - FAB WO2 ANTI-AMYLOID-BETA ANTIBODY FAB FRAGMENT
	Cell	:	HYBRIDOMA
	Chains	:	K, L
	Engineered	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	SERUM FREE MEDIUM (INVITROGEN)

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	F	H	K	L
Biological Unit 1 (1x)	:	A			H		L
Biological Unit 2 (1x)	:		B	F		K

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4F37)

(no "Site" information available for 4F37)

Asymmetric Unit

No.	Residues
1	F:22	-	F:97
2	F:152	-	F:207
3	H:22	-	H:97
4	H:152	-	H:207
5	K:23	-	K:93
6	K:139	-	K:199
7	L:23	-	L:93
8	L:139	-	L:199

Asymmetric Unit

No.	Residues
1	His A:63	-	Pro A:64
2	Ser A:80	-	Pro A:81
3	His B:63	-	Pro B:64
4	Phe F:158	-	Pro F:159
5	Glu F:160	-	Pro F:161
6	Trp F:200	-	Pro F:201
7	Phe H:158	-	Pro H:159
8	Glu H:160	-	Pro H:161
9	Trp H:200	-	Pro H:201
10	Thr K:7	-	Pro K:8
11	Pro K:49	-	Asn K:50
12	Val K:99	-	Pro K:100
13	Tyr K:145	-	Pro K:146
14	Thr L:7	-	Pro L:8
15	Pro L:49	-	Asn L:50
16	Val L:99	-	Pro L:100
17	Tyr L:145	-	Pro L:146

(no "SAP(SNP)/Variant" information available for 4F37)

(no "PROSITE Motif" information available for 4F37)

(no "Exon" information available for 4F37)

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:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh....hhhhhh........hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4f37 A   1 DAEFRHDSGYEVHHQKSELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKITEHPDGTDLIYYPSDNRDDSPEGIVKEIKEWRAANGKPGFKQ 102
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....................hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhh........hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4f37 B   1 DAEFRHDSGYEVHHQKSELKNSISDYTEAEFVQLLKEIEKENVAATDDVLDVLLEHFVKITEHPDGTDLIYYPSDNRDDSPEGIVKEIKEWRAANGKPGFKQ 102
                                    10        20        30        40        50        60        70        80        90       100

Chain F from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......ee.......ee..ee.........eeeeeee......eeeeee.....eee.........eee......eee.....hhhhh.eeeeeeee....hhhhheeeee......ee........................ee..eeee......................eeeee....eeeee..ee.............................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f37 F   1 QVTLKESGPGILQPSQTLSLTCSFSGFSLRTSRVGVSWIRQPSGKGLEWLAHIYWDDDKRYNPSLESRLTISKDTSRNQVFLKITSVDTADTATYYCARRGFYGRKYEVNHFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSESITCNVAHPASSTKVDKKIVPR 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain H from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...ee....eeeeeeee..........eeeeeee......eeeeee...............ee..ee....eeeeeee..hhhhheeeeeeee..................eeeee........eeeee...........eeeeeeee....................ee...eee..eee.eeeeee.............................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f37 H   1 QVTLKESGPGILQPSQTLSLTCSFSGFSLRTSRVGVSWIRQPSGKGLEWLAHIYWDDDKRYNPSLESRLTISKDTSRNQVFLKITSVDTADTATYYCARRGFYGRKYEVNHFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSESITCNVAHPASSTKVDKKIVPR 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain K from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d4f37k1 K:1-112 automated matches                                                                               d4f37k2 K:113-218 automated matches                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eee......eeee.ee..............eee........................eeeee....eeeee........eeeee.............eeee...........ee....hhhhhh.eeeeeee........eee...........................eeeeeee.............eee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f37 K   1 DIVMTQTPLSLPVSLGDQASISCRSSQTILHSNGNTYLEWYLQKPGQSPNLLIYKVSKRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSRVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d4f37l1 L:1-112 automated matches                                                                               d4f37l2 L:113-218 automated matches                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....ee.....eeeeeee............eeeeee.......eeee...ee...........ee..eeeeee........eeeeeee...........eeeee.......eee....hhhhh....eee..eeeee.......................ee........eeee..eee..hhhhhh........................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f37 L   1 DIVMTQTPLSLPVSLGDQASISCRSSQTILHSNGNTYLEWYLQKPGQSPNLLIYKVSKRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSRVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Mouse (Mus musculus) [TaxId: 10090] (309)

1a	d4f37k2	K:113-218
1b	d4f37l2	L:113-218

Family: V set domains (antibody variable domain-like) (1919)

Protein domain: automated matches (311)

Mouse (Mus musculus) [TaxId: 10090] (112)

2a	d4f37k1	K:1-112
2b	d4f37l1	L:1-112

(no "CATH Domain" information available for 4F37)

(no "Pfam Domain" information available for 4F37)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4f37)

	Sites
(no "Sites" information available for 4f37)

	Cis Peptide Bonds
		Glu F:160 - Pro F:161	[ RasMol ]
		Glu H:160 - Pro H:161	[ RasMol ]
		His A:63 - Pro A:64	[ RasMol ]
		His B:63 - Pro B:64	[ RasMol ]
		Phe F:158 - Pro F:159	[ RasMol ]
		Phe H:158 - Pro H:159	[ RasMol ]
		Pro K:49 - Asn K:50	[ RasMol ]
		Pro L:49 - Asn L:50	[ RasMol ]
		Ser A:80 - Pro A:81	[ RasMol ]
		Thr K:7 - Pro K:8	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Trp F:200 - Pro F:201	[ RasMol ]
		Trp H:200 - Pro H:201	[ RasMol ]
		Tyr K:145 - Pro K:146	[ RasMol ]
		Tyr L:145 - Pro L:146	[ RasMol ]
		Val K:99 - Pro K:100	[ RasMol ]
		Val L:99 - Pro L:100	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	4f37
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		Orientation in Membranes	:	OPM
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	A2NHM3_MOUSE \| A2NHM3
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	GCAA_MOUSE \| P01863
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	IMM7_ECOLX \| Q03708
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (17, 17)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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