4YXK - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ELK PRION PROTEIN COMPLEXED WITH POM1 FAB

Authors :   P. K. Baral, M. Swayampakula, M. N. G. James

Date :   23 Mar 15 (Deposition) - 23 Sep 15 (Release) - 14 Oct 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.81

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

Keywords :   Prion, Antibody, Immune System Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. K. Baral, M. Swayampakula, A. Aguzzi, M. N. James
X-Ray Structural And Molecular Dynamical Studies Of The Globular Domains Of Cow, Deer, Elk And Syrian Hamster Prion Proteins.
J. Struct. Biol. V. 192 37 2015
PubMed-ID: 26320075 | Reference-DOI: 10.1016/J.JSB.2015.08.014

Molecule 1 - MAJOR PRION PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PRNP, PRP
	Organism Common	:	NORTH AMERICAN ELK
	Organism Scientific	:	CERVUS ELAPHUS NELSONI
	Organism Taxid	:	9864
	Synonym	:	PRP

Molecule 2 - POM1 FAB HEAVY CHAIN
	Chains	:	H
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Taxid	:	10090
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - POM1 FAB LIGHT CHAIN
	Chains	:	L
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Taxid	:	10090
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3
Asymmetric Unit	:	A	H	L
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:169 , SER H:195 , GLU L:79 , GLU L:81	binding site for residue NA L 301

Asymmetric Unit

No.	Residues
1	H:22	-	H:96
2	H:145	-	H:200
3	L:23	-	L:88
4	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Phe H:151	-	Pro H:152
2	Glu H:153	-	Pro H:154
3	Trp H:193	-	Pro H:194
4	Ser L:7	-	Pro L:8
5	Trp L:94	-	Pro L:95
6	Tyr L:140	-	Pro L:141

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

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

(no "Exon" information available for 4YXK)

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:101
                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee............hhhhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 4yxk A 122 GGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYNNQNTFVHDCVNITVKQHTVTTTTKGENFTETDIKMMERVVEQMCITQYQRESE 222
                                   131       141       151       161       171       181       191       201       211       221

Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhh.eeeeee.........ee...eeeee.............................eeee.................eee...ee....eee.eee.................hhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yxk H   1 QVQLQQSGTELVMPGASVKMSCKASGYTFTDYWMHWVKQRPGQGLEWIGSIDPSDSYTSHNEKFKGKATLTVDESSSTAYMQLSSLTSEDSAVYFCSRSGYGYYAMEYWGQGTSVTVSSAKTTPPSVYPLAPGGGATNSMVTLGCLVKGYFPEPVTVTWNSGSLSGGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeee.............eeee....eeeeee...hhhhh.eeeeee......ee...eeeee.........eee..hhhhhh......eee.............................................................................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yxk L   1 DIVLTQSPAILSVSPGERVSFSCRASQNIGTSIHWYQQRTNESPRLIIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQSNTWPYTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSETDQDSKDSTYSMSSTLTLTKDEYERHNTYTCEATHKTSTSPIVKSFNRNE 213
                                    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 '\|'

(no "SCOP Domain" information available for 4YXK)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu H:153 - Pro H:154	[ RasMol ]
		Phe H:151 - Pro H:152	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Trp H:193 - Pro H:194	[ RasMol ]
		Trp L:94 - Pro L:95	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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

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	PRIO_CEREN \| P67986	:	1xyw 3fva

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (4, 4)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (8, 8)

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