1OJY - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   DECAY ACCELERATING FACTOR (CD55): THE STRUCTURE OF AN INTACT HUMAN COMPLEMENT REGULATOR.

Authors :   P. Lukacik, P. Roversi, J. White, D. Esser, G. P. Smith, J. Billington, P. A. Williams, P. M. Rudd, M. R. Wormald, M. D. M. Crispin, C. M. Radclif R. A. Dwek, D. J. Evans, B. P. Morgan, R. A. G. Smith, S. M. Lea

Date :   16 Jul 03 (Deposition) - 07 Jan 04 (Release) - 21 Sep 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Regulator Of Complement Pathway, Regulator Of Complement, Decay Acceleration Of C3/C5 Convertases, Pathogen Receptor, Short Consensus Repeat Domains, Plasma, Glycoprotein, Membrane, Gpi-Anchor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Lukacik, P. Roversi, J. White, D. Esser, G. P. Smith, J. Billington, P. A. Williams, P. M. Rudd, M. R. Wormald, D. J. Harvey, M. D. M. Crispin, C. M. Radcliffe, R. A. Dwek, D. J. Evans, B. P. Morgan, R. A. G. Smith, S. M. Lea
Complement Regulation At The Molecular Level: The Structure Of Decay-Accelerating Factor
Proc. Natl. Acad. Sci. Usa V. 101 1279 2004
PubMed-ID: 14734808 | Reference-DOI: 10.1073/PNAS.0307200101
(for further references see the PDB file header)

Molecule 1 - COMPLEMENT DECAY-ACCELERATING FACTOR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	FOUR EXTRACELLULAR SCR DOMAINS, RESIDUES 35-285
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	MODELLED GLYCEROLS, ACETATES AND SULPHATES FROM CRYSTALLISATION BUFFER
	Other Details - Source	:	HUMAN SEQUENCE EXPRESSED IN E.COLI.
	Synonym	:	DAF, CR, CD55

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 13)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	GOL	6	Ligand/Ion	GLYCEROL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:134 , ILE A:154 , PHE A:156 , SER A:170 , TRP A:181 , ASP A:183 , PRO A:184 , LEU A:185	BINDING SITE FOR RESIDUE ACT A1254
02	AC2	SOFTWARE	PRO B:134 , ILE B:154 , PHE B:156 , SER B:170 , TRP B:181 , ASP B:183 , PRO B:184 , LEU B:185	BINDING SITE FOR RESIDUE ACT B1255
03	AC3	SOFTWARE	TYR A:213 , ARG A:214 , TYR C:213 , ARG C:214 , TYR C:234 , THR C:236 , VAL C:237 , ASN C:238	BINDING SITE FOR RESIDUE SO4 C1254
04	AC4	SOFTWARE	PRO C:134 , ILE C:154 , PHE C:156 , SER C:170 , TRP C:181 , ASP C:183 , PRO C:184 , LEU C:185	BINDING SITE FOR RESIDUE ACT C1256
05	AC5	SOFTWARE	ARG A:138 , GLN C:215 , SER C:216	BINDING SITE FOR RESIDUE SO4 C1257
06	AC6	SOFTWARE	TYR B:213 , ARG B:214 , TYR D:213 , ARG D:214 , THR D:236 , VAL D:237 , ASN D:238	BINDING SITE FOR RESIDUE SO4 D1255
07	AC7	SOFTWARE	PRO D:134 , ILE D:154 , PHE D:156 , SER D:170 , TRP D:181 , ASP D:183 , PRO D:184 , LEU D:185	BINDING SITE FOR RESIDUE ACT D1256
08	AC8	SOFTWARE	ARG B:214 , GLN B:215 , SER B:216 , GLN D:141 , ASN D:159 , THR D:160 , HOH D:2024	BINDING SITE FOR RESIDUE GOL B1256
09	AC9	SOFTWARE	ARG A:214 , GLN A:215 , SER A:216 , GLN C:141 , ASN C:159 , THR C:160	BINDING SITE FOR RESIDUE GOL C1255
10	BC1	SOFTWARE	PHE C:156 , SER C:157 , CYS C:158 , LEU C:164 , ASP C:240	BINDING SITE FOR RESIDUE GOL C1258
11	BC2	SOFTWARE	PHE D:156 , SER D:157 , CYS D:158 , LYS D:163 , LEU D:164 , ASP D:240	BINDING SITE FOR RESIDUE GOL D1257
12	BC3	SOFTWARE	PRO D:7 , ASP D:9 , VAL D:10 , ALA D:13 , GLN D:14 , PRO D:15	BINDING SITE FOR RESIDUE GOL D1258
13	BC4	SOFTWARE	ARG A:252 , ARG B:138 , GLN D:215 , SER D:216	BINDING SITE FOR RESIDUE GOL D1259

Asymmetric Unit

No.	Residues
1	A:4	-	A:49
2	A:33	-	A:62
3	A:66	-	A:113
4	A:97	-	A:126
5	A:131	-	A:172
6	A:158	-	A:188
7	A:193	-	A:235
8	A:221	-	A:251
9	B:4	-	B:49
10	B:33	-	B:62
11	B:66	-	B:113
12	B:97	-	B:126
13	B:131	-	B:172
14	B:158	-	B:188
15	B:193	-	B:235
16	B:221	-	B:251
17	C:4	-	C:49
18	C:33	-	C:62
19	C:66	-	C:113
20	C:97	-	C:126
21	C:131	-	C:172
22	C:158	-	C:188
23	C:193	-	C:235
24	C:221	-	C:251
25	D:4	-	D:49
26	D:33	-	D:62
27	D:66	-	D:113
28	D:97	-	D:126
29	D:131	-	D:172
30	D:158	-	D:188
31	D:193	-	D:235
32	D:221	-	D:251

Asymmetric Unit

No.	Residues
1	Glu A:18	-	Gly A:19
2	Gln A:79	-	Pro A:80
3	Pro A:99	-	Gly A:100
4	Asn A:238	-	Asn A:239
5	Glu B:18	-	Gly B:19
6	Gln B:79	-	Pro B:80
7	Pro B:99	-	Gly B:100
8	Asn B:238	-	Asn B:239
9	Met C:1	-	Gln C:2
10	Leu C:17	-	Glu C:18
11	Glu C:18	-	Gly C:19
12	Gln C:79	-	Pro C:80
13	Pro C:99	-	Gly C:100
14	Asn C:238	-	Asn C:239
15	Leu D:17	-	Glu D:18
16	Glu D:18	-	Gly D:19
17	Gln D:79	-	Pro D:80
18	Pro D:99	-	Gly D:100
19	Asn D:238	-	Asn D:239

Asymmetric Unit (6, 24)

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

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

Biological Unit 1 (6, 12)

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

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

Biological Unit 2 (6, 12)

								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/D	R	20	L
2	UniProt	VAR_001998	R	52	P	DAF_HUMAN	Polymorphism	28371588	B/D	R	20	P
3	UniProt	VAR_001999	L	82	R	DAF_HUMAN	Polymorphism	147474393	B/D	L	50	R
4	UniProt	VAR_002000	S	199	L	DAF_HUMAN	Polymorphism	56283594	B/D	S	167	L
5	UniProt	VAR_002001	A	227	P	DAF_HUMAN	Polymorphism	60822373	B/D	A	195	P
6	UniProt	VAR_015884	R	240	H	DAF_HUMAN	Polymorphism	199705465	B/D	R	208	H

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

Asymmetric Unit (1, 16)

	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	16	A:64-128 B:64-128 C:64-128 D:64-128 A:3-62 B:3-62 C:3-62 D:3-62 A:129-190 B:129-190 C:129-190 D:129-190 A:191-253 B:191-253 C:191-253 D:191-253

Biological Unit 1 (1, 8)

	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	8	A:64-128 - C:64-128 - A:3-62 - C:3-62 - A:129-190 - C:129-190 - A:191-253 - C:191-253 -

Biological Unit 2 (1, 8)

	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	8	- B:64-128 - D:64-128 - B:3-62 - D:3-62 - B:129-190 - D:129-190 - B:191-253 - D:191-253

Asymmetric Unit (7, 28)

	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	4	A:2-2 B:2-2 C:1-2 D:2-2	1 1 2 1
1.3	ENST00000367064	3	ENSE00001443405	chr1:207495727-207495912	186	DAF_HUMAN	34-96	63	4	A:2-64 B:2-64 C:2-64 D:2-64	63 63 63 63
1.4b	ENST00000367064	4b	ENSE00001443404	chr1:207497904-207498095	192	DAF_HUMAN	96-160	65	4	A:64-128 B:64-128 C:64-128 D:64-128	65 65 65 65
1.5	ENST00000367064	5	ENSE00001069638	chr1:207498967-207499066	100	DAF_HUMAN	160-193	34	4	A:128-161 B:128-161 C:128-161 D:128-161	34 34 34 34
1.6	ENST00000367064	6	ENSE00001069637	chr1:207500097-207500182	86	DAF_HUMAN	193-222	30	4	A:161-190 B:161-190 C:161-190 D:161-190	30 30 30 30
1.7	ENST00000367064	7	ENSE00000960173	chr1:207504453-207504641	189	DAF_HUMAN	222-285	64	4	A:190-253 B:190-253 C:190-253 D:190-253	64 64 64 64
1.8b	ENST00000367064	8b	ENSE00001041396	chr1:207510038-207510163	126	DAF_HUMAN	285-327	43	4	A:253-253 B:253-254 C:253-253 D:253-254	1 2 1 2
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 A from PDB  Type:PROTEIN  Length:252
 aligned with DAF_HUMAN | P08174 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:252
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283  
            DAF_HUMAN    34 GDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDIEEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRG 285
               SCOP domains d1ojya1 A:2-64 Complement decay-accelerating factor (Daf, CD55)d1ojya2 A:65-128                                                d1ojya3 A:129-190                                             d1ojya4 A:191-253                                               SCOP domains
               CATH domains 1ojyA01 A:2-64 Complement Module, domain 1                     1ojyA02 A:65-128 Complement Module, domain 1                    1ojyA03 A:129-191 Complement Module, domain 1                  1ojyA04 A:192-253 Complement Module, domain 1                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee........eee.......ee...eeeeee...eee......eeeee...ee......eee..........eee..hhhhh.......eeeeee...eee......eee.............eee...........eeeee........eeeeee...eeee...eeeeeee..eeee.....eeee...........eeee..........eeeeee....eee...eeeee......ee.....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: A:3-62 UniProt: 34-94                            -SUSHI  PDB: A:64-128 UniProt: 96-160                             SUSHI  PDB: A:129-190 UniProt: 161-222                        SUSHI  PDB: A:191-253 UniProt: 223-285                          PROSITE
           Transcript 1 (1) 1-------------------------------------------------------------Exon 1.4b  PDB: A:64-128 UniProt: 96-160                         --------------------------------Exon 1.6  PDB: A:161-190      --------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: A:2-64 UniProt: 34-96                           ---------------------------------------------------------------Exon 1.5  PDB: A:128-161          ----------------------------Exon 1.7  PDB: A:190-253 UniProt: 222-285                        Transcript 1 (2)
                 1ojy A   2 QDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDIEEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRG 253
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with DAF_HUMAN | P08174 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:253
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
            DAF_HUMAN    34 GDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDIEEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRGK 286
               SCOP domains d1ojyb1 B:2-64 Complement decay-accelerating factor (Daf, CD55)d1ojyb2 B:65-128                                                d1ojyb3 B:129-190                                             d1ojyb4 B:191-254                                                SCOP domains
               CATH domains 1ojyB01 B:2-64 Complement Module, domain 1                     1ojyB02 B:65-128 Complement Module, domain 1                    1ojyB03 B:129-191 Complement Module, domain 1                  1ojyB04 B:192-254 Complement Module, domain 1                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........eee.......ee...eeeeee...eee......eeeee...ee......eee..........eee..hhhhh.......eeeeee...eee......eee.............eee...........eeeee........eeeeee...eeee...eeeeeee..eeee.....eeee...........eeee..........eeeeee....eee...eeeee......ee.....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: B:3-62 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) 1-------------------------------------------------------------Exon 1.4b  PDB: B:64-128 UniProt: 96-160                         --------------------------------Exon 1.6  PDB: B:161-190      --------------------------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: B:2-64 UniProt: 34-96                           ---------------------------------------------------------------Exon 1.5  PDB: B:128-161          ----------------------------Exon 1.7  PDB: B:190-253 UniProt: 222-285                       - Transcript 1 (2)
                 1ojy B   2 QDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDIEEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRGC 254
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

Chain C from PDB  Type:PROTEIN  Length:253
 aligned with DAF_HUMAN | P08174 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:253
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282   
            DAF_HUMAN    33 WGDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDIEEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRG 285
               SCOP domains d1ojyc1 C:1-64 Complement decay-accelerating factor (Daf, CD55) d1ojyc2 C:65-128                                                d1ojyc3 C:129-190                                             d1ojyc4 C:191-253                                               SCOP domains
               CATH domains 1ojyC01 C:1-64 Complement Module, domain 1                      1ojyC02 C:65-128 Complement Module, domain 1                    1ojyC03 C:129-191 Complement Module, domain 1                  1ojyC04 C:192-253 Complement Module, domain 1                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee........eee.......ee...eeeeee...eee......eeeee...ee......eee..........eee..............eeeeee...eee......eee.............eee...........eeee.........eeeeee...eeee...eeeeeee..eeee.....eeee...........eeee..........eeeeee....eeeee.eeeee......ee.....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: C:3-62 UniProt: 34-94                            -SUSHI  PDB: C:64-128 UniProt: 96-160                             SUSHI  PDB: C:129-190 UniProt: 161-222                        SUSHI  PDB: C:191-253 UniProt: 223-285                          PROSITE
           Transcript 1 (1) 1.-------------------------------------------------------------Exon 1.4b  PDB: C:64-128 UniProt: 96-160                         --------------------------------Exon 1.6  PDB: C:161-190      --------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -Exon 1.3  PDB: C:2-64 UniProt: 34-96                           ---------------------------------------------------------------Exon 1.5  PDB: C:128-161          ----------------------------Exon 1.7  PDB: C:190-253 UniProt: 222-285                        Transcript 1 (2)
                 1ojy C   1 MQDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDIEEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRG 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain D from PDB  Type:PROTEIN  Length:253
 aligned with DAF_HUMAN | P08174 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:253
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
            DAF_HUMAN    34 GDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDIEEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRGK 286
               SCOP domains d1ojyd1 D:2-64 Complement decay-accelerating factor (Daf, CD55)d1ojyd2 D:65-128                                                d1ojyd3 D:129-190                                             d1ojyd4 D:191-254                                                SCOP domains
               CATH domains 1ojyD01 D:2-64 Complement Module, domain 1                     1ojyD02 D:65-128 Complement Module, domain 1                    1ojyD03 D:129-191 Complement Module, domain 1                  1ojyD04 D:192-254 Complement Module, domain 1                   CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD01 D:193-251                                    --- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD02 D:193-251                                    --- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD03 D:193-251                                    --- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD04 D:193-251                                    --- Pfam domains (4)
           Pfam domains (5) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD05 D:193-251                                    --- Pfam domains (5)
           Pfam domains (6) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD06 D:193-251                                    --- Pfam domains (6)
           Pfam domains (7) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD07 D:193-251                                    --- Pfam domains (7)
           Pfam domains (8) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD08 D:193-251                                    --- Pfam domains (8)
           Pfam domains (9) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD09 D:193-251                                    --- Pfam domains (9)
          Pfam domains (10) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD10 D:193-251                                    --- Pfam domains (10)
          Pfam domains (11) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD11 D:193-251                                    --- Pfam domains (11)
          Pfam domains (12) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD12 D:193-251                                    --- Pfam domains (12)
          Pfam domains (13) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD13 D:193-251                                    --- Pfam domains (13)
          Pfam domains (14) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD14 D:193-251                                    --- Pfam domains (14)
          Pfam domains (15) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD15 D:193-251                                    --- Pfam domains (15)
          Pfam domains (16) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Sushi-1ojyD16 D:193-251                                    --- Pfam domains (16)
         Sec.struct. author .ee........eee.......ee...eeeeee...eee......eeeee...ee......eee..........eee..............eeeeee...eee......eee.............eee...........eeee.........eeeeee...eeee...eeeeeee..eeee.....eeee...........eeee..........eeeeee...eeeeee.eeeee......ee.....eeee. Sec.struct. author
             SAPs(SNPs) (1) ------------------L-----------------------------R--------------------------------------------------------------------------------------------------------------------L---------------------------P------------H---------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE SUSHI  PDB: D:3-62 UniProt: 34-94                            -SUSHI  PDB: D:64-128 UniProt: 96-160                             SUSHI  PDB: D:129-190 UniProt: 161-222                        SUSHI  PDB: D:191-253 UniProt: 223-285                         - PROSITE
           Transcript 1 (1) 1-------------------------------------------------------------Exon 1.4b  PDB: D:64-128 UniProt: 96-160                         --------------------------------Exon 1.6  PDB: D:161-190      --------------------------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) Exon 1.3  PDB: D:2-64 UniProt: 34-96                           ---------------------------------------------------------------Exon 1.5  PDB: D:128-161          ----------------------------Exon 1.7  PDB: D:190-253 UniProt: 222-285                       - Transcript 1 (2)
                 1ojy D   2 QDCGLPPDVPNAQPALEGRTSFPEDTVITYKCEESFVKIPGEKDSVICLKGSQWSDIEEFCNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRGC 254
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

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: Small proteins (3458)

Fold: Complement control module/SCR domain (70)

Superfamily: Complement control module/SCR domain (70)

Family: Complement control module/SCR domain (67)

Protein domain: Complement decay-accelerating factor (Daf, CD55) (18)

Human (Homo sapiens) [TaxId: 9606] (18)

1a	d1ojya1	A:2-64
1b	d1ojya2	A:65-128
1c	d1ojya3	A:129-190
1d	d1ojya4	A:191-253
1e	d1ojyb1	B:2-64
1f	d1ojyb2	B:65-128
1g	d1ojyb3	B:129-190
1h	d1ojyb4	B:191-254
1i	d1ojyc1	C:1-64
1j	d1ojyc2	C:65-128
1k	d1ojyc3	C:129-190
1l	d1ojyc4	C:191-253
1m	d1ojyd1	D:2-64
1n	d1ojyd2	D:65-128
1o	d1ojyd3	D:129-190
1p	d1ojyd4	D:191-254

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: Complement Module; domain 1 (62)

Homologous Superfamily: Complement Module, domain 1 (60)

Human (Homo sapiens) (46)

1a	1ojyA04	A:192-253
1b	1ojyC04	C:192-253
1c	1ojyB04	B:192-254
1d	1ojyD04	D:192-254
1e	1ojyA03	A:129-191
1f	1ojyB03	B:129-191
1g	1ojyC03	C:129-191
1h	1ojyD03	D:129-191
1i	1ojyA01	A:2-64
1j	1ojyB01	B:2-64
1k	1ojyD01	D:2-64
1l	1ojyC01	C:1-64
1m	1ojyA02	A:65-128
1n	1ojyB02	B:65-128
1o	1ojyC02	C:65-128
1p	1ojyD02	D:65-128

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Sushi] (50)

Family: Sushi (50)

Homo sapiens (Human) (42)

1a	Sushi-1ojyD01	D:193-251
1b	Sushi-1ojyD02	D:193-251
1c	Sushi-1ojyD03	D:193-251
1d	Sushi-1ojyD04	D:193-251
1e	Sushi-1ojyD05	D:193-251
1f	Sushi-1ojyD06	D:193-251
1g	Sushi-1ojyD07	D:193-251
1h	Sushi-1ojyD08	D:193-251
1i	Sushi-1ojyD09	D:193-251
1j	Sushi-1ojyD10	D:193-251
1k	Sushi-1ojyD11	D:193-251
1l	Sushi-1ojyD12	D:193-251
1m	Sushi-1ojyD13	D:193-251
1n	Sushi-1ojyD14	D:193-251
1o	Sushi-1ojyD15	D:193-251
1p	Sushi-1ojyD16	D:193-251

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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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	1ojy
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1h03	HUMAN CD55 DOMAINS 3 & 4
1h04	HUMAN CD55 DOMAINS 3 & 4
1h2p	HUMAN CD55 DOMAINS 3 & 4
1h2q	HUMAN CD55 DOMAINS 3 & 4
1m11	STRUCTURAL MODEL OF HUMAN DECAY-ACCELERATING FACTOR BOUNDTO ECHOVIRUS 7 FROM CRYO- ELECTRON MICROSCOPY
1nwv	SOLUTION STRUCTURE OF A FUNCTIONALLY ACTIVE COMPONENT OFDECAY ACCELERATING FACTOR
1ojv	DECAY ACCELERATING FACTOR: THE STRUCTURE OF AN INTACT HUMAN COMPLEMENT REGULATOR.
1ojw	DECAY ACCELERATING FACTOR: THE STRUCTURE OF AN INTACT HUMAN COMPLEMENT REGULATOR.
1ok1	DECAY ACCELERATING FACTOR: THE STRUCTURE OF AN INTACT HUMAN COMPLEMENT REGULATOR.
1ok2	DECAY ACCELERATING FACTOR: THE STRUCTURE OF AN INTACT HUMAN COMPLEMENT REGULATOR.
1ok3	DECAY ACCELERATING FACTOR: THE STRUCTURE OF AN INTACT HUMAN COMPLEMENT REGULATOR.
1ok9	DECAY ACCELERATING FACTOR: THE STRUCTURE OF AN INTACT HUMAN COMPLEMENT REGULATOR.
1uot	HUMAN CD55 DOMAINS 3 & 4
1upn	COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (13, 13)

SS Bonds (32, 32)

Cis Peptide Bonds (19, 19)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 24)

PROSITE Motifs (1, 16)

Exons (7, 28)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 16)

CATH Domains (1, 16)

Pfam Domains (1, 16)

Gene Ontology (28, 28)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File