3J24 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   CRYOEM RECONSTRUCTION OF COMPLEMENT DECAY-ACCELERATING FACTOR

Authors :   J. D. Yoder, S. H. Hafenstein

Date :   17 Aug 12 (Deposition) - 26 Sep 12 (Release) - 14 Nov 12 (Revision)

Method :   ELECTRON MICROSCOPY

Resolution :   9.00

Chains :   Asym. Unit : B
Biol. Unit 1: B  (60x)

Keywords :   Blood Group Antigen, Complement Pathway, Glycoprotein, Gpi-Anchor, Immune Response, Innate Immunity, Lipoprotein, Membrane, Sushi, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Yoder, J. O. Cifuente, J. Pan, J. M. Bergelson, S. Hafenstein
The Crystal Structure Of A Coxsackievirus B3-Rd Variant And A Refined 9-Angstrom Cryo-Electron Microscopy Reconstructio Of The Virus Complexed With Decay-Accelerating Factor (Daf) Provide A New Footprint Of Daf On The Virus Surface.
J. Virol. V. 86 12571 2012
PubMed-ID: 22973031 | Reference-DOI: 10.1128/JVI.01592-12

Molecule 1 - COMPLEMENT DECAY-ACCELERATING FACTOR
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	FOUR EXTRACELLULAR SCR DOMAINS (UNP RESIDUES 35-285)
	Gene	:	CD55, CR, DAF
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric Unit	:	B
Biological Unit 1 (60x)	:	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3J24)

(no "Site" information available for 3J24)

Asymmetric Unit

No.	Residues
1	B:4	-	B:49
2	B:33	-	B:62
3	B:66	-	B:113
4	B:97	-	B:126
5	B:131	-	B:172
6	B:158	-	B:188
7	B:193	-	B:235
8	B:221	-	B:251

Asymmetric Unit

No.	Residues
1	Gln B:79	-	Pro B:80
2	Pro B:99	-	Gly B:100

Asymmetric Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_001997	R	52	L	DAF_HUMAN	Polymorphism	28371588	B	R	20	L
2	UniProt	VAR_001998	R	52	P	DAF_HUMAN	Polymorphism	28371588	B	R	20	P
3	UniProt	VAR_001999	L	82	R	DAF_HUMAN	Polymorphism	147474393	B	L	50	R
4	UniProt	VAR_002000	S	199	L	DAF_HUMAN	Polymorphism	56283594	B	S	167	L
5	UniProt	VAR_002001	A	227	P	DAF_HUMAN	Polymorphism	60822373	B	A	195	P
6	UniProt	VAR_015884	R	240	H	DAF_HUMAN	Polymorphism	199705465	B	R	208	H

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

Biological Unit 1 (6, 360)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_001997	R	52	L	DAF_HUMAN	Polymorphism	28371588	B	R	20	L
2	UniProt	VAR_001998	R	52	P	DAF_HUMAN	Polymorphism	28371588	B	R	20	P
3	UniProt	VAR_001999	L	82	R	DAF_HUMAN	Polymorphism	147474393	B	L	50	R
4	UniProt	VAR_002000	S	199	L	DAF_HUMAN	Polymorphism	56283594	B	S	167	L
5	UniProt	VAR_002001	A	227	P	DAF_HUMAN	Polymorphism	60822373	B	A	195	P
6	UniProt	VAR_015884	R	240	H	DAF_HUMAN	Polymorphism	199705465	B	R	208	H

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SUSHI	PS50923	Sushi/CCP/SCR domain profile.	DAF_HUMAN	96-160 34-94 161-222 223-285	3	B:64-128 - B:129-190 B:191-253

Biological Unit 1 (1, 180)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SUSHI	PS50923	Sushi/CCP/SCR domain profile.	DAF_HUMAN	96-160 34-94 161-222 223-285	180	B:64-128 - B:129-190 B:191-253

Asymmetric Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000367064	1a	ENSE00001840627	chr1:207494853-207495210	358	DAF_HUMAN	1-34	34	0	-	-
1.3	ENST00000367064	3	ENSE00001443405	chr1:207495727-207495912	186	DAF_HUMAN	34-96	63	1	B:3-64	62
1.4b	ENST00000367064	4b	ENSE00001443404	chr1:207497904-207498095	192	DAF_HUMAN	96-160	65	1	B:64-128	65
1.5	ENST00000367064	5	ENSE00001069638	chr1:207498967-207499066	100	DAF_HUMAN	160-193	34	1	B:128-161	34
1.6	ENST00000367064	6	ENSE00001069637	chr1:207500097-207500182	86	DAF_HUMAN	193-222	30	1	B:161-190	30
1.7	ENST00000367064	7	ENSE00000960173	chr1:207504453-207504641	189	DAF_HUMAN	222-285	64	1	B:190-253	64
1.8b	ENST00000367064	8b	ENSE00001041396	chr1:207510038-207510163	126	DAF_HUMAN	285-327	43	1	B:253-253	1
1.8d	ENST00000367064	8d	ENSE00001253047	chr1:207510674-207510754	81	DAF_HUMAN	327-354	28	0	-	-
1.9	ENST00000367064	9	ENSE00001432766	chr1:207512742-207512762	21	DAF_HUMAN	354-361	8	0	-	-
1.15f	ENST00000367064	15f	ENSE00001631743	chr1:207532891-207534311	1421	DAF_HUMAN	361-381	21	0	-	-

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 B from PDB  Type:PROTEIN  Length:251
 aligned with DAF_HUMAN | P08174 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:251
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284 
            DAF_HUMAN    35 DCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDIEEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRG 285
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee............eeeeee...eee......eeeee...ee......eee..........eee..hhhhh.......eeeeee...eee......eee.............eee...........eeee.........eeeeee...eeee...eeeeeee..eeee.....eeee...........eeee..........eeeeee....eee...eeeeee....eee.....eee. Sec.struct. author
             SAPs(SNPs) (1) -----------------L-----------------------------R--------------------------------------------------------------------------------------------------------------------L---------------------------P------------H--------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------P----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE SUSHI  PDB: - UniProt: 34-94                                -SUSHI  PDB: B:64-128 UniProt: 96-160                             SUSHI  PDB: B:129-190 UniProt: 161-222                        SUSHI  PDB: B:191-253 UniProt: 223-285                          PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:3-64 UniProt: 34-96 [INCOMPLETE]             ---------------------------------------------------------------Exon 1.5  PDB: B:128-161          ----------------------------Exon 1.7  PDB: B:190-253 UniProt: 222-285                        Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------Exon 1.4b  PDB: B:64-128 UniProt: 96-160                         --------------------------------Exon 1.6  PDB: B:161-190      --------------------------------------------------------------1 Transcript 1 (2)
                 3j24 B   3 DCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDIEEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRG 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252

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 3J24)

(no "CATH Domain" information available for 3J24)

(no "Pfam Domain" information available for 3J24)

Asymmetric Unit(hide GO term definitions)

Chain B (DAF_HUMAN | P08174)

molecular function
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	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:0001618	virus receptor activity	Combining with a virus component and mediating entry of the virus into the cell.
biological process
	GO:0035743	CD4-positive, alpha-beta T cell cytokine production	Any process that contributes to cytokine production by a CD4-positive, alpha-beta T cell.
	GO:0006888	ER to Golgi vesicle-mediated transport	The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
	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:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0045916	negative regulation of complement activation	Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation.
	GO:2000516	positive regulation of CD4-positive, alpha-beta T cell activation	Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell activation.
	GO:2000563	positive regulation of CD4-positive, alpha-beta T cell proliferation	Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell proliferation.
	GO:0007204	positive regulation of cytosolic calcium ion concentration	Any process that increases the concentration of calcium ions in the cytosol.
	GO:0030449	regulation of complement activation	Any process that modulates the frequency, rate or extent of complement activation.
	GO:0031664	regulation of lipopolysaccharide-mediated signaling pathway	Any process that modulates the frequency, rate or extent of signaling in response to detection of lipopolysaccharide.
	GO:0045730	respiratory burst	A phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	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:0033116	endoplasmic reticulum-Golgi intermediate compartment membrane	The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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: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: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.
	GO:0030133	transport vesicle	Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

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	Ligands, Modified Residues, Ions
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(no "Sites" information available for 3j24)

	Cis Peptide Bonds
		Gln B:79 - Pro B:80	[ RasMol ]
		Pro B:99 - Gly B:100	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3j24
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 6)

PROSITE Motifs (1, 3)

Exons (6, 6)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (28, 28)

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