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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF ICSM 18 (ANTI-PRP THERAPEUTIC ANTIBODY) FAB FRAGMENT COMPLEXED WITH HUMAN PRP FRAGMENT 119-231

Authors :   S. V. Antonyuk, C. R. Trevitt, R. W. Strange, G. S. Jackson, D. Sangar, M. Batchelor, S. Jones, T. Georgiou, S. Cooper, C. Fraser, A. Khalili- A. R. Clarke, S. S. Hasnain, J. Collinge

Date :   23 Jan 09 (Deposition) - 03 Feb 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Fab, Prp, Prion, Membrane, Gpi-Anchor, Lipoprotein, Golgi Apparatus, Disease Mutation, Immune System, Glycoprotein, Cell Membrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. V. Antonyuk, C. R. Trevitt, R. W. Strange, G. S. Jackson, D. Sangar, M. Batchelor, S. Cooper, C. Fraser, S. Jones, T. Georgiou, A. Khalili-Shirazi, A. R. Clarke, S. S. Hasnain, J. Collinge
Crystal Structure Of Human Prion Protein Bound To A Therapeutic Antibody.
Proc. Natl. Acad. Sci. Usa V. 106 2554 2009
PubMed-ID: 19204296 | Reference-DOI: 10.1073/PNAS.0809170106

Molecule 1 - MAJOR PRION PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 119-231
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PRP27-30, PRP33-35C, ASCR, PRP

Molecule 2 - ICSM 18-ANTI-PRP THERAPEUTIC FAB HEAVY CHAIN
	Chains	:	H
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - ICSM 18-ANTI-PRP THERAPEUTIC FAB LIGHT CHAIN
	Chains	:	L
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3
Asymmetric/Biological Unit	:	A	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:136 , TYR H:60 , ARG H:65	BINDING SITE FOR RESIDUE SO4 A 300

Asymmetric/Biological Unit

No.	Residues
1	A:179	-	A:214
2	H:22	-	H:96
3	H:142	-	H:197
4	L:23	-	L:87
5	L:133	-	L:193

Asymmetric/Biological Unit

No.	Residues
1	Asn H:54	-	Asn H:55
2	Phe H:148	-	Pro H:149
3	Glu H:150	-	Pro H:151
4	Trp H:190	-	Pro H:191
5	Ser L:7	-	Pro L:8
6	Asn L:93	-	Pro L:94
7	Tyr L:139	-	Pro L:140

Asymmetric/Biological Unit (21, 21)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_073722	G	127	V	PRIO_HUMAN	Polymorphism	267606980	A	G	127	V
02	UniProt	VAR_006467	M	129	V	PRIO_HUMAN	Polymorphism	1799990	A	M	129	V
03	UniProt	VAR_014264	G	131	V	PRIO_HUMAN	Disease (GSD)	74315410	A	G	131	V
04	UniProt	VAR_006468	N	171	S	PRIO_HUMAN	Polymorphism	16990018	A	N	171	S
05	UniProt	VAR_006469	D	178	N	PRIO_HUMAN	Disease (FFI)	74315403	A	D	178	N
06	UniProt	VAR_006470	V	180	I	PRIO_HUMAN	Disease (CJD)	74315408	A	V	180	I
07	UniProt	VAR_006471	T	183	A	PRIO_HUMAN	Disease (SENF)	74315411	A	T	183	A
08	UniProt	VAR_008746	H	187	R	PRIO_HUMAN	Disease (GSD)	74315413	A	H	187	R
09	UniProt	VAR_008748	T	188	K	PRIO_HUMAN	Unclassified	---	A	T	188	K
10	UniProt	VAR_008747	T	188	R	PRIO_HUMAN	Polymorphism	372878791	A	T	188	R
11	UniProt	VAR_008749	E	196	K	PRIO_HUMAN	Disease (CJD)	---	A	E	196	K
12	UniProt	VAR_006472	F	198	S	PRIO_HUMAN	Disease (GSD)	74315405	A	F	198	S
13	UniProt	VAR_006473	E	200	K	PRIO_HUMAN	Disease (CJD)	28933385	A	E	200	K
14	UniProt	VAR_008750	D	202	N	PRIO_HUMAN	Disease (GSD)	761807915	A	D	202	N
15	UniProt	VAR_008751	V	203	I	PRIO_HUMAN	Unclassified (CJD)	776593792	A	V	203	I
16	UniProt	VAR_006474	R	208	H	PRIO_HUMAN	Disease (CJD)	74315412	A	R	208	H
17	UniProt	VAR_006475	V	210	I	PRIO_HUMAN	Disease (CJD)	74315407	A	V	210	I
18	UniProt	VAR_008752	E	211	Q	PRIO_HUMAN	Disease (CJD)	398122370	A	E	211	Q
19	UniProt	VAR_008753	Q	212	P	PRIO_HUMAN	Disease (GSD)	751882709	A	Q	212	P
20	UniProt	VAR_006476	Q	217	R	PRIO_HUMAN	Disease (GSD)	74315406	A	Q	217	R
21	UniProt	VAR_006477	E	219	K	PRIO_HUMAN	Polymorphism	1800014	A	E	219	K

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

Asymmetric/Biological Unit (2, 2)

	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:191-197
2	PRION_2	PS00706	Prion protein signature 2.	PRIO_HUMAN	200-218	1	A:200-218

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000379440	1c	ENSE00001957346	chr20:4666882-4667158	277	PRIO_HUMAN	-	0	0	-	-
1.2e	ENST00000379440	2e	ENSE00001928116	chr20:4679857-4682236	2380	PRIO_HUMAN	1-257	257	1	A:125-223	99

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:99
 aligned with PRIO_HUMAN | P04156 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:99
                                   134       144       154       164       174       184       194       204       214         
           PRIO_HUMAN   125 LGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQ 223
               SCOP domains d2w9ea_ A: automated matches                                                                        SCOP domains
               CATH domains 2w9eA00 A:125-223 Major Prion Protein                                                               CATH domains
               Pfam domains ---------Prion-2w9eA01 A:134-223                                                                    Pfam domains
         Sec.struct. author ....ee............hhhhhhhhhhhhhhh....ee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) --V-V-V---------------------------------------S------N-I--A---RK-------K-S-K-NI----H-IQP----R-K---- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------R----------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------------------PRION_2            ----- PROSITE
               Transcript 1 Exon 1.2e  PDB: A:125-223 UniProt: 1-257 [INCOMPLETE]                                               Transcript 1
                 2w9e A 125 LGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQ 223
                                   134       144       154       164       174       184       194       204       214

Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2w9eH01 H:1-116 Immunoglobulins                                                                                     2w9eH02 H:117-215 Immunoglobulins                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee.......eeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee.........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w9e H   1 EVQLQQSGPELVKPGSSVKISCKASRNTFTDYNLDWVKQSHGKTLEWIGNVYPNNGVTGYNQKFRGKATLTVDKSSSTAYMELHSLTSEDSAVYYCALYYYDVSYWGQGTLVTVSSAKTTPPSVYPLAPGSAAQTNSVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQSVTCNVAHPASSTAVDKKIAPA 215
                                    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:212
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:212
                                                                                                                                       1                                                                                                        
                                     -         -         -         -         -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        93       103  
           IGKC_MOUSE     - -----------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 105
               SCOP domains d2w9el1 L:1-109 automated matches                                                                            d2w9el2 L:110-212 automated matches                                                                     SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------2w9eL02 L:108-210 Immunoglobulins                                                                      -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeee..eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh..eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w9e L   1 QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMHWYQQKSGTSPKRWIYDTSKLASGVPARFSGSGSGTSYSLTISSMEAEDAATYFCHQWRSNPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTGGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 212
                                    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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Major Prion Protein (62)

Homologous Superfamily: Major Prion Protein (62)

Human (Homo sapiens) (28)

2w9eA00

A:125-223

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

2a	2w9eL02	L:108-210
2b	2w9eH02	H:117-215
2c	2w9eH01	H:1-116

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Prion] (32)

Family: Prion (32)

Homo sapiens (Human) (7)

Prion-2w9eA01

A:134-223

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PRIO_HUMAN | P04156)

molecular function
	GO:0043008	ATP-dependent 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) using energy from the hydrolysis of ATP.
	GO:0051087	chaperone binding	Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0044325	ion channel binding	Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
	GO:0005521	lamin binding	Interacting selectively and non-covalently with lamin; any of a group of intermediate-filament proteins that form the fibrous matrix on the inner surface of the nuclear envelope.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	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).
	GO:0015631	tubulin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules.
biological process
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0007050	cell cycle arrest	A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
	GO:0006878	cellular copper ion homeostasis	Any process involved in the maintenance of an internal steady state of copper ions at the level of a cell.
	GO:0071280	cellular response to copper ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a copper ion stimulus.
	GO:0035690	cellular response to drug	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0007611	learning or memory	The acquisition and processing of information and/or the storage and retrieval of this information over time.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0050860	negative regulation of T cell receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0046007	negative regulation of activated T cell proliferation	Any process that stops, prevents or reduces the rate or extent of activated T cell proliferation.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0070885	negative regulation of calcineurin-NFAT signaling cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of the calcineurin-NFAT signaling cascade.
	GO:0032689	negative regulation of interferon-gamma production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
	GO:0032700	negative regulation of interleukin-17 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines.
	GO:0032703	negative regulation of interleukin-2 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production.
	GO:0001933	negative regulation of protein phosphorylation	Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
	GO:0043433	negative regulation of sequence-specific DNA binding transcription factor activity	Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:1901379	regulation of potassium ion transmembrane transport	Any process that modulates the frequency, rate or extent of potassium ion transmembrane transport.
	GO:0032880	regulation of protein localization	Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
	GO:0046686	response to cadmium ion	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 cadmium (Cd) ion stimulus.
	GO:0046688	response to copper ion	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 copper ion stimulus.
	GO:0006979	response to oxidative stress	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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0019898	extrinsic component of membrane	The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	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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	Cis Peptide Bonds
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		Asn L:93 - Pro L:94	[ RasMol ]
		Glu H:150 - Pro H:151	[ RasMol ]
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		Tyr L:139 - Pro L:140	[ RasMol ]

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	2w9e
		Family and Domain Information	:	ProDom \| SYSTERS
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1e1g	HUMAN PRION PROTEIN VARIANT M166V
1e1j	HUMAN PRION PROTEIN VARIANT M166V
1e1p	HUMAN PRION PROTEIN VARIANT S170N
1e1s	HUMAN PRION PROTEIN VARIANT S170N
1e1u	HUMAN PRION PROTEIN VARIANT R220K
1e1w	HUMAN PRION PROTEIN VARIANT R220K
1fkc	HUMAN PRION PROTEIN (MUTANT E200K) FRAGMENT 90-231
1fo7	HUMAN PRION PROTEIN MUTANT E200K FRAGMENT 90 -231
1h0l	HUMAN PRION PROTEIN 121-230 M166C/E221C
1hjm	HUMAN PRION PROTEIN AT PH 7.0
1hjn	HUMAN PRION PROTEIN AT PH 7.0
1i4m	CRYSTAL STRUCTURE OF THE HUMAN PRION PROTEIN REVEALS AMECHANISM FOR OLIGOMERIZATION
1oeh	HUMAN PRION PROTEIN 61-68
1oei	HUMAN PRION PROTEIN 61-84
1qlx	HUMAN PRION PROTEIN
1qlz	HUMAN PRION PROTEIN STRUCTURE OF FAB FRAGMENT OF THE ICSM 18 - ANTI-PRP THERAPEUTIC ANTIBODY AT 1.65 A RESOLUTION.
1qm0	HUMAN PRION PROTEIN FRAGMENT 90-230
1qm1	HUMAN PRION PROTEIN FRAGMENT 90-230
1qm2	HUMAN PRION PROTEIN FRAGMENT 121-230
1qm3	HUMAN PRION PROTEIN FRAGMENT 121-230

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (5, 5)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (21, 21)

PROSITE Motifs (2, 2)

Exons (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (2, 4)

Pfam Domains (1, 1)

Gene Ontology (56, 57)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File