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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURAL RECOGNITION AND FUNCTIONAL ACTIVATION OF FCRR BY INNATE PENTRAXINS

Authors :   J. Lu, L. L. Marnell, K. D. Marjon, C. Mold, T. W. Du Clos, P. D. Sun

Date :   16 May 08 (Deposition) - 11 Nov 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Complex Structure, Sap, Fc Riia, Fc Receptor Activation, Pentraxins, Amyloid, Glycoprotein, Lectin, Metal-Binding, Secreted, Cell Membrane, Igg-Binding Protein, Immunoglobulin Domain, Membrane, Phosphoprotein, Receptor, Transmembrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Lu, L. L. Marnell, K. D. Marjon, C. Mold, T. W. Du Clos, P. D. Sun
Structural Recognition And Functional Activation Of Fcgamma By Innate Pentraxins.
Nature V. 456 989 2008
PubMed-ID: 19011614 | Reference-DOI: 10.1038/NATURE07468

Molecule 1 - SERUM AMYLOID P-COMPONENT
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SAP, 9.5S ALPHA-1-GLYCOPROTEIN, SERUM AMYLOID P-COMPONENT(1- 203)

Molecule 2 - LOW AFFINITY IMMUNOGLOBULIN GAMMA FC REGION RECEPTOR II-A
	Chains	:	F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	FCGR2A, CD32, FCG2, FCGR2A1, IGFR2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IGG FC RECEPTOR II-A, FC-GAMMA RII-A, FC-GAMMA-RIIA, FCRII- A, CDW32

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)	E (1x)	F (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 22)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	16	Ligand/Ion	SULFATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:78 , ARG A:120 , GLN A:121	BINDING SITE FOR RESIDUE SO4 A 205
02	AC2	SOFTWARE	HIS A:19 , ASN A:21 , ARG A:193	BINDING SITE FOR RESIDUE SO4 A 206
03	AC3	SOFTWARE	LEU A:43 , SER A:44 , ARG A:45 , LYS B:83	BINDING SITE FOR RESIDUE SO4 A 207
04	AC4	SOFTWARE	HIS B:78 , LEU B:119 , ARG B:120	BINDING SITE FOR RESIDUE SO4 B 205
05	AC5	SOFTWARE	HIS B:19 , ASN B:21 , LYS B:130 , ARG B:193 , PRO F:2 , GLN F:69 , SER F:74 , LEU F:75	BINDING SITE FOR RESIDUE SO4 B 206
06	AC6	SOFTWARE	ASP B:42 , LEU B:43 , SER B:44 , ARG B:45 , LYS C:83	BINDING SITE FOR RESIDUE SO4 B 207
07	AC7	SOFTWARE	LEU C:119 , ARG C:120 , HOH C:213	BINDING SITE FOR RESIDUE SO4 C 205
08	AC8	SOFTWARE	HIS C:19 , ASN C:21 , ARG C:193	BINDING SITE FOR RESIDUE SO4 C 206
09	AC9	SOFTWARE	LEU C:43 , SER C:44 , ARG C:45 , LYS D:83	BINDING SITE FOR RESIDUE SO4 C 207
10	BC1	SOFTWARE	HIS D:78 , LEU D:119 , ARG D:120	BINDING SITE FOR RESIDUE SO4 D 205
11	BC2	SOFTWARE	HIS D:19 , ASN D:21 , GLY D:141 , ARG D:193	BINDING SITE FOR RESIDUE SO4 D 206
12	BC3	SOFTWARE	ASP D:42 , LEU D:43 , SER D:44 , ARG D:45 , LYS E:83	BINDING SITE FOR RESIDUE SO4 D 207
13	BC4	SOFTWARE	HIS E:78 , LEU E:119 , ARG E:120	BINDING SITE FOR RESIDUE SO4 E 205
14	BC5	SOFTWARE	HIS E:19 , ASN E:21 , ARG E:193	BINDING SITE FOR RESIDUE SO4 E 206
15	BC6	SOFTWARE	LYS A:83 , LEU E:43 , SER E:44 , ARG E:45	BINDING SITE FOR RESIDUE SO4 E 207
16	BC7	SOFTWARE	HIS F:94 , LEU F:95 , GLU F:96	BINDING SITE FOR RESIDUE SO4 F 178
17	BC8	SOFTWARE	ARG A:38 , PRO A:91 , ASN A:110 , TRP A:203 , SER F:34 , ASP F:35	BINDING SITE FOR RESIDUE GOL F 179
18	BC9	SOFTWARE	ASN A:32 , GLU A:99	BINDING SITE FOR RESIDUE NAG A 208
19	CC1	SOFTWARE	PRO A:25 , GLN B:31 , ASN B:32 , GLU B:99	BINDING SITE FOR RESIDUE NAG B 208
20	CC2	SOFTWARE	GLN C:31 , ASN C:32 , GLU C:99	BINDING SITE FOR RESIDUE NAG C 208
21	CC3	SOFTWARE	GLN D:31 , ASN D:32	BINDING SITE FOR RESIDUE NAG D 208
22	CC4	SOFTWARE	GLN E:31 , ASN E:32 , HOH E:209	BINDING SITE FOR RESIDUE NAG E 208

Asymmetric Unit

No.	Residues
1	A:36	-	A:95
2	B:36	-	B:95
3	C:36	-	C:95
4	D:36	-	D:95
5	E:36	-	E:95
6	F:26	-	F:68
7	F:107	-	F:151

Asymmetric Unit

No.	Residues
1	Phe A:88	-	Pro A:89
2	Phe B:88	-	Pro B:89
3	Phe C:88	-	Pro C:89
4	Phe D:88	-	Pro D:89
5	Phe E:88	-	Pro E:89
6	Glu F:10	-	Pro F:11

Asymmetric Unit (6, 18)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_054857	Q	63	R	FCG2A_HUMAN	Polymorphism	9427398	F	Q	27	R
2	UniProt	VAR_054858	M	140	V	FCG2A_HUMAN	Polymorphism	4986941	F	M	104	V
3	UniProt	VAR_035814	G	141	S	SAMP_HUMAN	Unclassified	---	A/B/C/D/E	G	122	S
4	UniProt	VAR_003955	H	167	R	FCG2A_HUMAN	Polymorphism	1801274	F	R	131	R
5	UniProt	VAR_006054	E	155	G	SAMP_HUMAN	Polymorphism	---	A/B/C/D/E	E	136	G
6	UniProt	VAR_006055	S	158	G	SAMP_HUMAN	Polymorphism	---	A/B/C/D/E	S	139	G

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

Biological Unit 1 (6, 18)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_054857	Q	63	R	FCG2A_HUMAN	Polymorphism	9427398	F	Q	27	R
2	UniProt	VAR_054858	M	140	V	FCG2A_HUMAN	Polymorphism	4986941	F	M	104	V
3	UniProt	VAR_035814	G	141	S	SAMP_HUMAN	Unclassified	---	A/B/C/D/E	G	122	S
4	UniProt	VAR_003955	H	167	R	FCG2A_HUMAN	Polymorphism	1801274	F	R	131	R
5	UniProt	VAR_006054	E	155	G	SAMP_HUMAN	Polymorphism	---	A/B/C/D/E	E	136	G
6	UniProt	VAR_006055	S	158	G	SAMP_HUMAN	Polymorphism	---	A/B/C/D/E	S	139	G

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

Asymmetric Unit (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PTX_2	PS51828	Pentraxin (PTX) domain profile.	SAMP_HUMAN	24-223	5	A:5-204 B:5-204 C:5-204 D:5-204 E:5-204
2	PTX_1	PS00289	Pentraxin domain signature.	SAMP_HUMAN	112-119	5	A:93-100 B:93-100 C:93-100 D:93-100 E:93-100

Biological Unit 1 (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PTX_2	PS51828	Pentraxin (PTX) domain profile.	SAMP_HUMAN	24-223	5	A:5-204 B:5-204 C:5-204 D:5-204 E:5-204
2	PTX_1	PS00289	Pentraxin domain signature.	SAMP_HUMAN	112-119	5	A:93-100 B:93-100 C:93-100 D:93-100 E:93-100

Asymmetric Unit (5, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000255040	1	ENSE00000904938	chr1:159557615-159557775	161	SAMP_HUMAN	1-22	22	5	A:1-3 B:1-3 C:1-3 D:1-3 E:1-3	3 3 3 3 3
1.2	ENST00000255040	2	ENSE00000904939	chr1:159557891-159558655	765	SAMP_HUMAN	22-223	202	5	A:3-204 B:3-204 C:3-204 D:3-204 E:3-204	202 202 202 202 202

2.1a	ENST00000271450	1a	ENSE00001170978	chr1:161475220-161475342	123	FCG2A_HUMAN	1-29	29	0	-	-
2.1g	ENST00000271450	1g	ENSE00000958752	chr1:161475777-161475797	21	FCG2A_HUMAN	29-36	8	0	-	-
2.1j	ENST00000271450	1j	ENSE00001651726	chr1:161476124-161476381	258	FCG2A_HUMAN	36-122	87	1	F:1-86	86
2.3a	ENST00000271450	3a	ENSE00001614571	chr1:161479610-161479864	255	FCG2A_HUMAN	122-207	86	1	F:86-171	86
2.4a	ENST00000271450	4a	ENSE00000958755	chr1:161480624-161480746	123	FCG2A_HUMAN	207-248	42	1	F:171-171	1
2.6a	ENST00000271450	6a	ENSE00001643425	chr1:161483685-161483722	38	FCG2A_HUMAN	248-260	13	0	-	-
2.8h	ENST00000271450	8h	ENSE00001170974	chr1:161487765-161489358	1594	FCG2A_HUMAN	261-317	57	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:204
 aligned with SAMP_HUMAN | P02743 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:204
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           SAMP_HUMAN    20 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 223
               SCOP domains d3d5oa_ A: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 3d5oA00 A:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee.........eeeeeeeee......eeeeeee.......eeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhh........ee.....eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: A:5-204 UniProt: 24-223                                                                                                                                                                      PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: A:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 3d5o A   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with SAMP_HUMAN | P02743 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:204
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           SAMP_HUMAN    20 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 223
               SCOP domains d3d5ob_ B: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 3d5oB00 B:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee.........eeeeeeeee......eeeeeee.......eeeeeee..eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee..................eeeeeeeee....hhhhhhhhhh.........hhhhh.eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: B:5-204 UniProt: 24-223                                                                                                                                                                      PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: B:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 3d5o B   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain C from PDB  Type:PROTEIN  Length:204
 aligned with SAMP_HUMAN | P02743 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:204
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           SAMP_HUMAN    20 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 223
               SCOP domains d3d5oc_ C: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 3d5oC00 C:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee........eeee..........eeeeeeee......eeeeeeee......eeeeeee..eeeeee...eeeee........eeeeeee.....eeeeee..ee...ee..........eeeee...........hhhhh...eeeeeeee....hhhhhhhhhhh.......ee.hhh.eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: C:5-204 UniProt: 24-223                                                                                                                                                                      PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: C:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 3d5o C   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain D from PDB  Type:PROTEIN  Length:204
 aligned with SAMP_HUMAN | P02743 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:204
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           SAMP_HUMAN    20 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 223
               SCOP domains d3d5od_ D: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 3d5oD00 D:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee.........eeeeeeeee......eeeeeee.......eeeeeee..eeeeee.....eee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhhh........ee.....eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: D:5-204 UniProt: 24-223                                                                                                                                                                      PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: D:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 3d5o D   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain E from PDB  Type:PROTEIN  Length:204
 aligned with SAMP_HUMAN | P02743 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:204
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
           SAMP_HUMAN    20 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 223
               SCOP domains d3d5oe_ E: Serum amyloid P component (SAP)                                                                                                                                                                   SCOP domains
               CATH domains 3d5oE00 E:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee.......eeee.........eeeeeeeee......eeeeeee.......eeeee....eeeeee..eeeeee........eeeeeeee....eeeeee..ee...ee...........eeee...........hhhhh..eeeeeeeee....hhhhhhhhh.........ee.hhh.eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------S-------------G--G----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PTX_2  PDB: E:5-204 UniProt: 24-223                                                                                                                                                                      PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------PTX_1   -------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: E:3-204 UniProt: 22-223                                                                                                                                                                     Transcript 1 (2)
                 3d5o E   1 HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV 204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain F from PDB  Type:PROTEIN  Length:171
 aligned with FCG2A_HUMAN | P12318 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:171
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206 
          FCG2A_HUMAN    37 APPKAVLKLEPPWINVLQEDSVTLTCQGARSPESDSIQWFHNGNLIPTHTQPSYRFKANNNDSGEYTCQTGQTSLSDPVHLTVLSEWLVLQTPHLEFQEGETIMLRCHSWKDKPLVKVTFFQNGKSQKFSHLDPTFSIPQANHSHSGDYHCTGNIGYTLFSSKPVTITVQV 207
               SCOP domains d3d5of1 F:1-85 automated matches                                                     d3d5of2 F:86-171 automated matches                                                     SCOP domains
               CATH domains 3d5oF01 F:1-86 Immunoglobulins                                                        3d5oF02 F:87-171 Immunoglobulins                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eee...eeeeeee.........eeeee..ee.......eeeee.hhhhheeeeeee........eeeeee...eee.....eee....eeeeeee.hhh..eeeeee.............eeee........eeeeeeee..........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------R----------------------------------------------------------------------------V--------------------------R---------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.1j  PDB: F:1-86 UniProt: 36-122 [INCOMPLETE]                                   ------------------------------------------------------------------------------------2 Transcript 2 (1)
           Transcript 2 (2) -------------------------------------------------------------------------------------Exon 2.3a  PDB: F:86-171 UniProt: 122-207                                              Transcript 2 (2)
                 3d5o F   1 APPKAVLKLEPPWINVLQEDSVTLTCQGARSPESDSIQWFHNGNLIPTHTQPSYRFKANNNDSGEYTCQTGQTSLSDPVHLTVLSEWLVLQTPHLEFQEGETIMLRCHSWKDKPLVKVTFFQNGKSQKFSRLDPTFSIPQANHSHSGDYHCTGNIGYTLFSSKPVTITVQV 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: Pentraxin (pentaxin) (18)

Protein domain: Serum amyloid P component (SAP) (12)

Human (Homo sapiens) [TaxId: 9606] (12)

1a	d3d5oa_	A:
1b	d3d5ob_	B:
1c	d3d5oc_	C:
1d	d3d5od_	D:
1e	d3d5oe_	E:

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: I set domains (152)

Protein domain: automated matches (23)

Human (Homo sapiens) [TaxId: 9606] (22)

2a	d3d5of1	F:1-85
2b	d3d5of2	F:86-171

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1a	3d5oF02	F:87-171
1b	3d5oF01	F:1-86

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.200, no name defined] (421)

Human (Homo sapiens) (49)

2a	3d5oA00	A:1-204
2b	3d5oB00	B:1-204
2c	3d5oC00	C:1-204
2d	3d5oD00	D:1-204
2e	3d5oE00	E:1-204

(no "Pfam Domain" information available for 3D5O)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (SAMP_HUMAN | P02743)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0001849	complement component C1q binding	Interacting selectively and non-covalently with the C1q component of the classical complement cascade.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
	GO:0046790	virion binding	Interacting selectively and non-covalently with a virion, either by binding to components of the capsid or the viral envelope.
biological process
	GO:0006953	acute-phase response	An acute inflammatory response that involves non-antibody proteins whose concentrations in the plasma increase in response to infection or injury of homeothermic animals.
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0051131	chaperone-mediated protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex, mediated by chaperone molecules that do not form part of the finished complex.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0044869	negative regulation by host of viral exo-alpha-sialidase activity	The process in which a host organism decreases viral exo-alpha-sialidase activity, the catalysis of the hydrolysis of peptide bonds in a protein.
	GO:0044871	negative regulation by host of viral glycoprotein metabolic process	A process in which a host organism stops, prevents or reduces the frequency, rate or extent of viral glycoprotein metabolic process.
	GO:0002674	negative regulation of acute inflammatory response	Any process that stops, prevents, or reduces the frequency, rate, or extent of an acute inflammatory response.
	GO:1903016	negative regulation of exo-alpha-sialidase activity	Any process that stops, prevents or reduces the frequency, rate or extent of exo-alpha-sialidase activity.
	GO:1903019	negative regulation of glycoprotein metabolic process	Any process that stops, prevents or reduces the frequency, rate or extent of glycoprotein metabolic process.
	GO:0045656	negative regulation of monocyte differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of monocyte differentiation.
	GO:0046597	negative regulation of viral entry into host cell	Any process that stops, prevents, or reduces the frequency, rate or extent of the entry of viral entry into a host cell.
	GO:0048525	negative regulation of viral process	Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant.
	GO:0061045	negative regulation of wound healing	Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
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: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:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	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.

Chain F (FCG2A_HUMAN | P12318)

molecular function
	GO:0019864	IgG binding	Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype.
	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).
biological process
	GO:0038096	Fc-gamma receptor signaling pathway involved in phagocytosis	An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
	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.
cellular component
	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:0016021	integral component of membrane	The component of a 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: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.

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	3d5o
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(no "Related Entries Specified in the PDB File" available for 3D5O)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 22)

Sites (22, 22)

SS Bonds (7, 7)

Cis Peptide Bonds (6, 6)

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SAPs(SNPs)/Variants (6, 18)

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Exons (5, 13)

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