3OL2 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   RECEPTOR-LIGAND STRUCTURE OF HUMAN SEMAPHORIN 4D WITH PLEXIN B1.

Authors :   B. J. C. Janssen, R. A. Robinson, F. Perez-Branguli, C. H. Bell, C. J. Mit C. Siebold, E. Y. Jones

Date :   25 Aug 10 (Deposition) - 13 Oct 10 (Release) - 05 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.99

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

Keywords :   Beta-Propeller, Signalling, Extacellular, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. J. Janssen, R. A. Robinson, F. Perez-Branguli, C. H. Bell, K. J. Mitchell, C. Siebold, E. Y. Jones
Structural Basis Of Semaphorin-Plexin Signalling.
Nature V. 467 1118 2010
PubMed-ID: 20877282 | Reference-DOI: 10.1038/NATURE09468

Molecule 1 - SEMAPHORIN-4D
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Fragment	:	EXTRACELLULAR DOMAINS
	Gene	:	SEMA4D, C9ORF164, CD100, SEMAJ
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BB18, A8, GR3

Molecule 2 - PLEXIN-B1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Fragment	:	EXTRACELLULAR DOMAINSL (1-2)
	Gene	:	PLXNB1, KIAA0407, PLXN5, SEP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SEMAPHORIN RECEPTOR SEP

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 16)

No.	Name	Count	Type	Full Name
1	BMA	3	Ligand/Ion	BETA-D-MANNOSE
2	NAG	13	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 32)

No.	Name	Count	Type	Full Name
1	BMA	6	Ligand/Ion	BETA-D-MANNOSE
2	NAG	26	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:49 , TYR A:111 , PRO A:160 , ASN A:492 , NAG A:1001	BINDING SITE FOR RESIDUE NAG A 1000
02	AC2	SOFTWARE	NAG A:1000 , BMA A:1002	BINDING SITE FOR RESIDUE NAG A 1001
03	AC3	SOFTWARE	NAG A:1001	BINDING SITE FOR RESIDUE BMA A 1002
04	AC4	SOFTWARE	ASN A:77 , SER A:79 , GLU A:80	BINDING SITE FOR RESIDUE NAG A 3000
05	AC5	SOFTWARE	ASN A:139 , THR A:141 , LEU A:146 , NAG A:4001	BINDING SITE FOR RESIDUE NAG A 4000
06	AC6	SOFTWARE	NAG A:4000	BINDING SITE FOR RESIDUE NAG A 4001
07	AC7	SOFTWARE	ASN A:329 , SER A:331 , NAG A:6001	BINDING SITE FOR RESIDUE NAG A 6000
08	AC8	SOFTWARE	NAG A:6000 , BMA A:6002	BINDING SITE FOR RESIDUE NAG A 6001
09	AC9	SOFTWARE	NAG A:6001	BINDING SITE FOR RESIDUE BMA A 6002
10	BC1	SOFTWARE	ASN A:319 , VAL A:320 , GLY A:321 , ASP A:417 , ASN A:419 , NAG A:8001	BINDING SITE FOR RESIDUE NAG A 8000
11	BC2	SOFTWARE	NAG A:8000	BINDING SITE FOR RESIDUE NAG A 8001
12	BC3	SOFTWARE	GLY A:171 , ASN A:191 , SER A:193 , NAG A:9001	BINDING SITE FOR RESIDUE NAG A 9000
13	BC4	SOFTWARE	NAG A:9000	BINDING SITE FOR RESIDUE NAG A 9001
14	BC5	SOFTWARE	ASP B:327 , ASP B:330 , ARG B:331 , ASN B:334 , ARG B:337 , NAG B:2001	BINDING SITE FOR RESIDUE NAG B 2000
15	BC6	SOFTWARE	NAG B:2000 , BMA B:2002	BINDING SITE FOR RESIDUE NAG B 2001
16	BC7	SOFTWARE	NAG B:2001	BINDING SITE FOR RESIDUE BMA B 2002

Asymmetric Unit

No.	Residues
1	A:97	-	A:108
2	A:126	-	A:135
3	A:257	-	A:370
4	A:281	-	A:326
5	A:503	-	A:520
6	A:509	-	A:553
7	A:512	-	A:529
8	A:576	-	A:624
9	B:79	-	B:88
10	B:111	-	B:119
11	B:252	-	B:377
12	B:268	-	B:322
13	B:340	-	B:364
14	B:482	-	B:499
15	B:488	-	B:533
16	B:491	-	B:508
17	B:502	-	B:514

Asymmetric Unit

No.	Residues
1	Val A:320	-	Gly A:321
2	Glu A:349	-	Gln A:350
3	Lys A:364	-	Pro A:365
4	Ser A:598	-	Pro A:599
5	Gly B:71	-	Pro B:72
6	Pro B:81	-	Pro B:82
7	Cys B:268	-	Glu B:269
8	Glu B:348	-	Asp B:349
9	Gly B:350	-	Thr B:351
10	Ser B:384	-	Pro B:385
11	Leu B:531	-	Gly B:532

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_030293	A	72	T	SEM4D_HUMAN	Polymorphism	13284404	A	A	72	T
2	UniProt	VAR_057175	A	327	T	SEM4D_HUMAN	Polymorphism	11526468	A	A	327	T
3	UniProt	VAR_050598	R	389	W	PLXB1_HUMAN	Polymorphism	34050056	B	R	389	W

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

Biological Unit 1 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_030293	A	72	T	SEM4D_HUMAN	Polymorphism	13284404	A	A	72	T
2	UniProt	VAR_057175	A	327	T	SEM4D_HUMAN	Polymorphism	11526468	A	A	327	T
3	UniProt	VAR_050598	R	389	W	PLXB1_HUMAN	Polymorphism	34050056	B	R	389	W

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

(no "PROSITE Motif" information available for 3OL2)

Asymmetric Unit (19, 19)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.4	ENST00000356444	4	ENSE00001424804	chr9:92070868-92070803	66	SEM4D_HUMAN	-	0	0	-	-
1.6b	ENST00000356444	6b	ENSE00001422645	chr9:92033352-92033278	75	SEM4D_HUMAN	-	0	0	-	-
1.7b	ENST00000356444	7b	ENSE00001419415	chr9:92033033-92032971	63	SEM4D_HUMAN	-	0	0	-	-
1.9d	ENST00000356444	9d	ENSE00001416368	chr9:92020614-92020266	349	SEM4D_HUMAN	1-36	36	1	A:24-36	13
1.10c	ENST00000356444	10c	ENSE00001405010	chr9:92017931-92017786	146	SEM4D_HUMAN	36-84	49	1	A:36-84	49
1.11	ENST00000356444	11	ENSE00001432732	chr9:92014253-92014191	63	SEM4D_HUMAN	85-105	21	1	A:85-105	21
1.12	ENST00000356444	12	ENSE00002193353	chr9:92011750-92011652	99	SEM4D_HUMAN	106-138	33	1	A:106-138	33
1.13	ENST00000356444	13	ENSE00001365232	chr9:92008570-92008477	94	SEM4D_HUMAN	139-170	32	1	A:139-170	32
1.14	ENST00000356444	14	ENSE00001381319	chr9:92007451-92007338	114	SEM4D_HUMAN	170-208	39	1	A:170-208	39
1.15	ENST00000356444	15	ENSE00001384069	chr9:92006330-92006179	152	SEM4D_HUMAN	208-258	51	1	A:208-258 (gaps)	51
1.16	ENST00000356444	16	ENSE00001383236	chr9:92003962-92003787	176	SEM4D_HUMAN	259-317	59	1	A:259-317	59
1.17a	ENST00000356444	17a	ENSE00001364475	chr9:92003707-92003551	157	SEM4D_HUMAN	317-369	53	1	A:317-369	53
1.18a	ENST00000356444	18a	ENSE00001384090	chr9:92002523-92002301	223	SEM4D_HUMAN	370-444	75	1	A:370-444	75
1.19	ENST00000356444	19	ENSE00001371945	chr9:92001397-92001282	116	SEM4D_HUMAN	444-482	39	1	A:444-482	39
1.20b	ENST00000356444	20b	ENSE00001383649	chr9:91996261-91996089	173	SEM4D_HUMAN	483-540	58	1	A:483-540	58
1.21	ENST00000356444	21	ENSE00001364259	chr9:91996013-91995970	44	SEM4D_HUMAN	540-555	16	1	A:540-555	16
1.22c	ENST00000356444	22c	ENSE00001364891	chr9:91994544-91992152	2393	SEM4D_HUMAN	555-862	308	1	A:555-648 (gaps)	94

2.3b	ENST00000358536	3b	ENSE00001668057	chr3:48470872-48470662	211	PLXB1_HUMAN	-	0	0	-	-
2.4a	ENST00000358536	4a	ENSE00001428482	chr3:48466742-48466690	53	PLXB1_HUMAN	-	0	0	-	-
2.5a	ENST00000358536	5a	ENSE00001206107	chr3:48466026-48464914	1113	PLXB1_HUMAN	1-369	369	1	B:23-369 (gaps)	347
2.6	ENST00000358536	6	ENSE00001080883	chr3:48464356-48464174	183	PLXB1_HUMAN	370-430	61	1	B:370-430	61
2.7a	ENST00000358536	7a	ENSE00001080893	chr3:48463868-48463740	129	PLXB1_HUMAN	431-473	43	1	B:431-473	43
2.8	ENST00000358536	8	ENSE00001080898	chr3:48463614-48463514	101	PLXB1_HUMAN	474-507	34	1	B:474-507	34
2.9	ENST00000358536	9	ENSE00001080910	chr3:48463215-48463083	133	PLXB1_HUMAN	507-551	45	1	B:507-533 (gaps)	27
2.10	ENST00000358536	10	ENSE00001080902	chr3:48462793-48462637	157	PLXB1_HUMAN	552-604	53	0	-	-
2.11	ENST00000358536	11	ENSE00001080906	chr3:48462365-48462257	109	PLXB1_HUMAN	604-640	37	0	-	-
2.12	ENST00000358536	12	ENSE00001080876	chr3:48462182-48462074	109	PLXB1_HUMAN	640-676	37	0	-	-
2.13c	ENST00000358536	13c	ENSE00001326499	chr3:48461666-48460986	681	PLXB1_HUMAN	677-903	227	0	-	-
2.13g	ENST00000358536	13g	ENSE00001673675	chr3:48460775-48460653	123	PLXB1_HUMAN	904-944	41	0	-	-
2.14	ENST00000358536	14	ENSE00001644091	chr3:48460448-48460326	123	PLXB1_HUMAN	945-985	41	0	-	-
2.15	ENST00000358536	15	ENSE00001632794	chr3:48459951-48459858	94	PLXB1_HUMAN	986-1017	32	0	-	-
2.16b	ENST00000358536	16b	ENSE00001689569	chr3:48459772-48459600	173	PLXB1_HUMAN	1017-1074	58	0	-	-
2.17	ENST00000358536	17	ENSE00001688877	chr3:48459471-48459320	152	PLXB1_HUMAN	1075-1125	51	0	-	-
2.18b	ENST00000358536	18b	ENSE00001630248	chr3:48457860-48457755	106	PLXB1_HUMAN	1125-1160	36	0	-	-
2.19	ENST00000358536	19	ENSE00001685598	chr3:48457576-48457440	137	PLXB1_HUMAN	1161-1206	46	0	-	-
2.20a	ENST00000358536	20a	ENSE00001604226	chr3:48457168-48456992	177	PLXB1_HUMAN	1206-1265	60	0	-	-
2.21c	ENST00000358536	21c	ENSE00001725709	chr3:48456756-48456585	172	PLXB1_HUMAN	1265-1322	58	0	-	-
2.22b	ENST00000358536	22b	ENSE00001726311	chr3:48456450-48456208	243	PLXB1_HUMAN	1323-1403	81	0	-	-
2.23c	ENST00000358536	23c	ENSE00001731310	chr3:48455480-48455304	177	PLXB1_HUMAN	1404-1462	59	0	-	-
2.23h	ENST00000358536	23h	ENSE00001788421	chr3:48455227-48455079	149	PLXB1_HUMAN	1463-1512	50	0	-	-
2.23j	ENST00000358536	23j	ENSE00001633158	chr3:48454578-48454478	101	PLXB1_HUMAN	1512-1546	35	0	-	-
2.24a	ENST00000358536	24a	ENSE00001749742	chr3:48454368-48454151	218	PLXB1_HUMAN	1546-1618	73	0	-	-
2.25	ENST00000358536	25	ENSE00001745479	chr3:48454029-48453851	179	PLXB1_HUMAN	1619-1678	60	0	-	-
2.26a	ENST00000358536	26a	ENSE00001731741	chr3:48453713-48453647	67	PLXB1_HUMAN	1678-1700	23	0	-	-
2.26c	ENST00000358536	26c	ENSE00001740702	chr3:48453418-48453272	147	PLXB1_HUMAN	1701-1749	49	0	-	-
2.27b	ENST00000358536	27b	ENSE00001769186	chr3:48452445-48452277	169	PLXB1_HUMAN	1750-1806	57	0	-	-
2.27d	ENST00000358536	27d	ENSE00001752233	chr3:48451967-48451864	104	PLXB1_HUMAN	1806-1840	35	0	-	-
2.28a	ENST00000358536	28a	ENSE00001597624	chr3:48451789-48451705	85	PLXB1_HUMAN	1841-1869	29	0	-	-
2.29b	ENST00000358536	29b	ENSE00001747202	chr3:48451486-48451314	173	PLXB1_HUMAN	1869-1926	58	0	-	-
2.30a	ENST00000358536	30a	ENSE00001685743	chr3:48451139-48450979	161	PLXB1_HUMAN	1927-1980	54	0	-	-
2.30d	ENST00000358536	30d	ENSE00001746046	chr3:48450884-48450737	148	PLXB1_HUMAN	1980-2029	50	0	-	-
2.31a	ENST00000358536	31a	ENSE00001798246	chr3:48448498-48448434	65	PLXB1_HUMAN	2030-2051	22	0	-	-
2.32a	ENST00000358536	32a	ENSE00001737780	chr3:48448305-48448230	76	PLXB1_HUMAN	2051-2076	26	0	-	-
2.33b	ENST00000358536	33b	ENSE00001624889	chr3:48447205-48447131	75	PLXB1_HUMAN	2077-2101	25	0	-	-
2.34c	ENST00000358536	34c	ENSE00001862726	chr3:48445997-48445263	735	PLXB1_HUMAN	2102-2135	34	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:614
 aligned with SEM4D_HUMAN | Q92854 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:625
                                    33        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       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643     
          SEM4D_HUMAN    24 FAPIPRITWEHREVHLVQFHEPDIYNYSALLLSEDKDTLYIGAREAVFAVNALNISEKQHEVYWKVSEDKKAKCAEKGKSKQTECLNYIRVLQPLSATSLYVCGTNAFQPACDHLNLTSFKFLGKNEDGKGRCPFDPAHSYTSVMVDGELYSGTSYNFLGSEPIISRNSSHSPLRTEYAIPWLNEPSFVFADVIRKSPDSPDGEDDRVYFFFTEVSVEYEFVFRVLIPRIARVCKGDQGGLRTLQKKWTSFLKARLICSRPDSGLVFNVLRDVFVLRSPGLKVPVFYALFTPQLNNVGLSAVCAYNLSTAEEVFSHGKYMQSTTVEQSHTKWVRYNGPVPKPRPGACIDSEARAANYTSSLNLPDKTLQFVKDHPLMDDSVTPIDNRPRLIKKDVNYTQIVVDRTQALDGTVYDVMFVSTDRGALHKAISLEHAVHIIEETQLFQDFEPVQTLLLSSKKGNRFVYAGSNSGVVQAPLAFCGKHGTCEDCVLARDPYCAWSPPTATCVALHQTESPSRGLIQEMSGDASVCPDKSKGSYRQHFFKHGGTAELKCSQKSNLARVFWKFQNGVLKAESPKYGLMGRKNLLIFNLSEGDSGVYQCLSEERVKNKTVFQVVAKHVLEVKV 648
               SCOP domains d3ol2a1 A:24-501 Semaphorin 4d                                                                                                                                                                                                                                                                                                                                                                                                                                                                d3ol2a2 A:502-555 Semaphorin 4d                            d3ol2a3 A:561-648 Semaphorin 4d Ig-like domain                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------Sema-3ol2A03 A:50-482                                                                                                                                                                                                                                                                                                                                                                                                                            -------------------PSI-3ol2A02 A:502-554                                -     --------ig-3ol2A01 A:569-626                                      ---------------------- Pfam domains
         Sec.struct. author .......eehhhhh..eee.........eeee.....eeeee...eeeeee......eeeeee...hhhhhhhhhh............eeeeee....eeeeee......eeeeee....ee....ee.............eeeee..eeeeeee.......eeeeee.....ee...........eeeeeeee..------....eeeeeeeee..........eeeeeeeee.................eeee...eehhhhee..eeeeeeee........eeeeeee.......eeeeeeeehhhhhhhhhhh..eeeeee...eeeeee..............hhhhhhh...hhhhhhhhhhhhhhhh........hhhhh..eeee...eeeeeeeeee.....eeeeeeeee...eeeeeeee..eeeeeeeee.........eeeee......eeeee....eeee...hhhhh.hhhhhhhh....eeee....eeee......hhhhh......hhhhh..-----.eeeee.....eee.........eeeeee..ee.......eeee...eeee...hhhhheeeeeeeeee....eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ------------Exon 1.10c  PDB: A:36-84 UniProt: 36-84          Exon 1.11            Exon 1.12  PDB: A:106-138        Exon 1.13  PDB: A:139-170       -------------------------------------Exon 1.15  PDB: A:208-258 (gaps) UniProt: 208-258  Exon 1.16  PDB: A:259-317 UniProt: 259-317                 ----------------------------------------------------Exon 1.18a  PDB: A:370-444 UniProt: 370-444                                --------------------------------------Exon 1.20b  PDB: A:483-540 UniProt: 483-540               --------------Exon 1.22c  PDB: A:555-648 (gaps) UniProt: 555-862 [INCOMPLETE]                                Transcript 1 (1)
           Transcript 1 (2) Exon 1.9d    -------------------------------------------------------------------------------------------------------------------------------------Exon 1.14  PDB: A:170-208              ------------------------------------------------------------------------------------------------------------Exon 1.17a  PDB: A:317-369 UniProt: 317-369          --------------------------------------------------------------------------Exon 1.19  PDB: A:444-482              ---------------------------------------------------------Exon 1.21       --------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3ol2 A  24 FAPIPRITWEHREVHLVQFHEPDIYNYSALLLSEDKDTLYIGAREAVFAVNALNISEKQHEVYWKVSEDKKAKCAEKGKSKQTECLNYIRVLQPLSATSLYVCGTNAFQPACDHLNLTSFKFLGKNEDGKGRCPFDPAHSYTSVMVDGELYSGTSYNFLGSEPIISRNSSHSPLRTEYAIPWLNEPSFVFADVIRK------GEDDRVYFFFTEVSVEYEFVFRVLIPRIARVCKGDQGGLRTLQKKWTSFLKARLICSRPDSGLVFNVLRDVFVLRSPGLKVPVFYALFTPQLNNVGLSAVCAYNLSTAEEVFSHGKYMQSTTVEQSHTKWVRYNGPVPKPRPGACIDSEARAANYTSSLNLPDKTLQFVKDHPLMDDSVTPIDNRPRLIKKDVNYTQIVVDRTQALDGTVYDVMFVSTDRGALHKAISLEHAVHIIEETQLFQDFEPVQTLLLSSKKGNRFVYAGSNSGVVQAPLAFCGKHGTCEDCVLARDPYCAWSPPTATCVALHQTESPSRGLIQEMSGDASVCPD-----YRQHFFKHGGTAELKCSQKSNLARVFWKFQNGVLKAESPKYGLMGRKNLLIFNLSEGDSGVYQCLSEERVKNKTVFQVVAKHVLEVKV 648
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     |   -  |    233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553 |     563       573       583       593       603       613       623       633       643     
                                                                                                                                                                                                                             219    226                                                                                                                                                                                                                                                                                                                                      555   561

Chain B from PDB  Type:PROTEIN  Length:496
 aligned with PLXB1_HUMAN | O43157 from UniProtKB/Swiss-Prot  Length:2135

    Alignment length:511
                                    32        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       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532 
          PLXB1_HUMAN    23 LPPTAFTPNGTYLQHLARDPTSGTLYLGATNFLFQLSPGLQLEATVSTGPVLDSRDCLPPVMPDECPQAQPTNNPNQLLLVSPGALVVCGSVHQGVCEQRRLGQLEQLLLRPERPGDTQYVAANDPAVSTVGLVAQGLAGEPLLFVGRGYTSRGVGGGIPPITTRALWPPDPQAAFSYEETAKLAVGRLSEYSHHFVSAFARGASAYFLFLRRDLQAQSRAFRAYVSRVCLRDQHYYSYVELPLACEGGRYGLIQAAAVATSREVAHGEVLFAAFSSAAPPTVGRPPSAAAGASGASALCAFPLDEVDRLANRTRDACYTREGRAEDGTEVAYIEYDVNSDCAQLPVDTLDAYPCGSDHTPSPMASRVPLEATPILEWPGIQLTAVAVTMEDGHTIAFLGDSQGQLHRVYLGPGSDGHPYSTQSIQQGSAVSRDLTFDGTFEHLYVMTQSTLLKVPVASCAQHLDCASCLAHRDPYCGWCVLLGRCSRRSECSRGQGPEQWLWSFQPELGC 533
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------Sema-3ol2B02 B:35-460                                                                                                                                                                                                                                                                                                                                                                                                                     --------------------PSI-3ol2B01 B:481-529                            ---- Pfam domains
         Sec.struct. author ....ee......eeeeee......eeeee..eeeee.....eeeeee...eee................eee...eeeeee...eeeeee.hhhh.eeeee..eeeeeee.....hhhhh.........eeeeeee.....eeeeeee....---......eeeee....hhhhh............hhhhhh.eeeeeeee..eeeeeeeee........eeeeeeeee.........eeeeee.......eeeeeeeee.---....eeeeeee....-----.....hhhhh.eeeeeeehhhhhhhhhhhhhhhhhh..........eee.............hhhhhh..........eee...ee....eee....eeeeeeeee..eeeeeeee...eeeeee..........eeee...........ee.....eeeee....eeeee..hhhhh.hhhhhhhh.....eee....eeehhhhh.----...eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.5a  PDB: B:23-369 (gaps) UniProt: 1-369 [INCOMPLETE]                                                                                                                                                                                                                                                                                                Exon 2.6  PDB: B:370-430 UniProt: 370-430                    Exon 2.7a  PDB: B:431-473 UniProt: 431-473 Exon 2.8  PDB: B:474-507          -------------------------- Transcript 2 (1)
           Transcript 2 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 2.9 UniProt: 507-551   Transcript 2 (2)
                 3ol2 B  23 LPPTAFTPNGTYLQHLARDPTSGTLYLGATNFLFQLSPGLQLEATVSTGPVLDSRDCLPPVMPDECPQAQPTNNPNQLLLVSPGALVVCGSVHQGVCEQRRLGQLEQLLLRPERPGDTQYVAANDPAVSTVGLVAQGLAGEPLLFVGRGYTS---GGGIPPITTRALWPPDPQAAFSYEETAKLAVGRLSEYSHHFVSAFARGASAYFLFLRRDLQAQSRAFRAYVSRVCLRDQHYYSYVELPLACEGGRYGLIQAAAVATS---AHGEVLFAAFSSAAP-----PPSAAAGASGASALCAFPLDEVDRLANRTRDACYTREGRAEDGTEVAYIEYDVNSDCAQLPVDTLDAYPCGSDHTPSPMASRVPLEATPILEWPGIQLTAVAVTMEDGHTIAFLGDSQGQLHRVYLGPGSDGHPYSTQSIQQGSAVSRDLTFDGTFEHLYVMTQSTLLKVPVASCAQHLDCASCLAHRDPYCGWCVLLGRCSRRSECS----PEQWLWSFQPELGC 533
                                    32        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 |   | 292       302     | 312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512  |    522       532 
                                                                                                                                                                                 174 178                                                                                                       284 288           302   308                                                                                                                                                                                                            515  520

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 "CATH Domain" information available for 3OL2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: ig (14)

Homo sapiens (Human) (11)

ig-3ol2A01

A:569-626

Clan: no clan defined [family: PSI] (9)

Family: PSI (9)

Homo sapiens (Human) (6)

2a	PSI-3ol2B01	B:481-529
2b	PSI-3ol2A02	A:502-554

Clan: no clan defined [family: Sema] (8)

Family: Sema (8)

Homo sapiens (Human) (4)

3a	Sema-3ol2B02	B:35-460
3b	Sema-3ol2A03	A:50-482

Asymmetric Unit(hide GO term definitions)

Chain A (SEM4D_HUMAN | Q92854)

molecular function
	GO:0045499	chemorepellent activity	Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a lower concentration of that signal.
	GO:0038191	neuropilin binding	Interacting selectively and non-covalently with a member of the neuropilin family.
	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:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0030215	semaphorin receptor binding	Interacting selectively and non-covalently with semaphorin receptors.
	GO:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0070486	leukocyte aggregation	The adhesion of one leukocyte to one or more other leukocytes via adhesion molecules.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0050919	negative chemotaxis	The directed movement of a motile cell or organism towards a lower concentration of a chemical.
	GO:0010693	negative regulation of alkaline phosphatase activity	Any process that decreases the frequency, rate or extent of alkaline phosphatase activity, the catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0048843	negative regulation of axon extension involved in axon guidance	Any process that stops, prevents, or reduces the frequency, rate or extent of axon extension involved in axon guidance.
	GO:0007162	negative regulation of cell adhesion	Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
	GO:0045668	negative regulation of osteoblast differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation.
	GO:0050732	negative regulation of peptidyl-tyrosine phosphorylation	Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0001755	neural crest cell migration	The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo.
	GO:0043931	ossification involved in bone maturation	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in the progression of the skeleton from its formation to its mature state.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0050772	positive regulation of axonogenesis	Any process that activates or increases the frequency, rate or extent of axonogenesis.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0048672	positive regulation of collateral sprouting	Any process that activates or increases the frequency, rate or extent of collateral sprouting.
	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0014068	positive regulation of phosphatidylinositol 3-kinase signaling	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:0001934	positive regulation of protein phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
	GO:0031344	regulation of cell projection organization	Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0048814	regulation of dendrite morphogenesis	Any process that modulates the frequency, rate or extent of dendrite morphogenesis.
	GO:0071526	semaphorin-plexin signaling pathway	A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand.
	GO:1900220	semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis	Any semaphorin-plexin signaling pathway that contributes to bone trabecula morphogenesis.
cellular component
	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: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: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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain B (PLXB1_HUMAN | O43157)

molecular function
	GO:0032794	GTPase activating protein binding	Interacting selectively and non-covalently with a GTPase activating protein.
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	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:0004872	receptor activity	Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
	GO:0017154	semaphorin receptor activity	Combining with a semaphorin, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
	GO:0030215	semaphorin receptor binding	Interacting selectively and non-covalently with semaphorin receptors.
	GO:0004888	transmembrane signaling receptor activity	Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
	GO:0048675	axon extension	Long distance growth of a single axon process involved in cellular development.
	GO:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0007162	negative regulation of cell adhesion	Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
	GO:0033689	negative regulation of osteoblast proliferation	Any process that stops, prevents or reduces the rate or extent of osteoblast proliferation.
	GO:0048812	neuron projection morphogenesis	The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
	GO:0043931	ossification involved in bone maturation	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in the progression of the skeleton from its formation to its mature state.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0050772	positive regulation of axonogenesis	Any process that activates or increases the frequency, rate or extent of axonogenesis.
	GO:0014068	positive regulation of phosphatidylinositol 3-kinase signaling	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:0043087	regulation of GTPase activity	Any process that modulates the rate of GTP hydrolysis by a GTPase.
	GO:0030334	regulation of cell migration	Any process that modulates the frequency, rate or extent of cell migration.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0051493	regulation of cytoskeleton organization	Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
	GO:0071526	semaphorin-plexin signaling pathway	A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand.
	GO:1902287	semaphorin-plexin signaling pathway involved in axon guidance	Any semaphorin-plexin signaling pathway that is involved in axon guidance.
	GO:1900220	semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis	Any semaphorin-plexin signaling pathway that contributes to bone trabecula morphogenesis.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	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: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: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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	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.
	GO:0002116	semaphorin receptor complex	A stable binary complex of a neurophilin and a plexin, together forming a functional semaphorin receptor.

Asymmetric Unit
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	Cis Peptide Bonds
		Cys B:268 - Glu B:269	[ RasMol ]
		Glu A:349 - Gln A:350	[ RasMol ]
		Glu B:348 - Asp B:349	[ RasMol ]
		Gly B:350 - Thr B:351	[ RasMol ]
		Gly B:71 - Pro B:72	[ RasMol ]
		Leu B:531 - Gly B:532	[ RasMol ]
		Lys A:364 - Pro A:365	[ RasMol ]
		Pro B:81 - Pro B:82	[ RasMol ]
		Ser A:598 - Pro A:599	[ RasMol ]
		Ser B:384 - Pro B:385	[ RasMol ]
		Val A:320 - Gly A:321	[ RasMol ]

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	3ol2
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	SEM4D_HUMAN \| Q92854
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UniProtKB/Swiss-Prot
	PLXB1_HUMAN \| O43157	:	2jph 2os6 2r2o 2rex 3hm6 3su8 3sua 5b4w
	SEM4D_HUMAN \| Q92854	:	1olz

1olz	SOLUBLE EXTRACELLULAR FRAGMENT, RESIDUES 22-677 OF SEMA4D
3okt	MOUSE PLEXIN A2, EXTRACELLULAR DOMAINS 1-4

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 16)

Sites (16, 16)

SS Bonds (17, 17)

Cis Peptide Bonds (11, 11)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (0, 0)

Exons (19, 19)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (0, 0)

Pfam Domains (3, 5)

Gene Ontology (56, 72)

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Related Entries Specified in the PDB File