8T6L

Cryo-EM structure of rat cardiac sodium channel NaV1.5 with batrachotoxin analog BTX-B

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A	Sodium channel protein type 5 subunit alpha,Green fluorescent protein	polymer	1874	213523.9	1	UniProt (P15389) UniProt (P42212) Pfam (PF00520) Pfam (PF06512) Pfam (PF01353) In PDB	Rattus norvegicus (Norway rat)	Sodium channel protein cardiac muscle subunit alpha,Sodium channel protein type V subunit alpha,Voltage-gated sodium channel subunit alpha Nav1.5
2	B	alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		748.7	1	In PDB
3	C, D	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		424.4	2	In PDB GlyTouCan (G42666HT)
4	E	alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	branched		910.8	1	In PDB GlyTouCan (G94626GC)
5	A	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	3	Chemie (NAG)
6	A	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine	non-polymer		760.1	10	Chemie (LBN)
7	A	CHOLESTEROL HEMISUCCINATE	non-polymer		486.7	11	Chemie (Y01)
8	A	(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en	non-polymer		544.8	2	Chemie (9Z9)
9	A	(1R)-1-[(5aR,7aR,9R,11aS,11bS,12R,13aR)-9,12-dihydroxy-2,11a-dimethyl-1,2,3,4,7a,8,9,10,11,11a,12,13-dodecahydro-7H-9,11b-epoxy-13a,5a-prop[1]enophenanthro[2,1-f][1,4]oxazepin-14-yl]ethyl benzoate	non-polymer		521.6	2	Chemie (YIJ)
10		water	water		18.0	1	Chemie (HOH)

Sequence modifications

A: 1 - 1931 (UniProt: P15389)

PDB	External Database	Details
Thr 33	Ala 33	engineered mutation
Asp 214	Gly 214	engineered mutation
-	Leu 462	deletion
-	Glu 463	deletion
-	Met 464	deletion
-	Ser 465	deletion
-	Pro 466	deletion
-	Leu 467	deletion
-	Ala 468	deletion
-	Pro 469	deletion
-	Val 470	deletion
-	Thr 471	deletion
-	Asn 472	deletion
-	His 473	deletion
-	Glu 474	deletion
-	Arg 475	deletion
-	Lys 476	deletion
-	Ser 477	deletion
-	Lys 478	deletion
-	Arg 479	deletion
-	Arg 480	deletion
-	Lys 481	deletion
-	Arg 482	deletion
-	Leu 483	deletion
-	Ser 484	deletion
-	Ser 485	deletion
-	Gly 486	deletion
-	Thr 487	deletion
-	Glu 488	deletion
-	Asp 489	deletion
-	Gly 490	deletion
-	Gly 491	deletion
-	Asp 492	deletion
-	Asp 493	deletion
-	Arg 494	deletion
-	Leu 495	deletion
-	Pro 496	deletion
-	Lys 497	deletion
-	Ser 498	deletion
-	Asp 499	deletion
-	Ser 500	deletion
-	Glu 501	deletion
-	Asp 502	deletion
-	Gly 503	deletion
-	Pro 504	deletion
-	Arg 505	deletion
-	Ala 506	deletion
-	Leu 507	deletion
-	Asn 508	deletion
-	Gln 509	deletion
-	Leu 510	deletion
-	Ser 511	deletion
-	Leu 512	deletion
-	Thr 513	deletion
-	His 514	deletion
-	Gly 515	deletion
-	Leu 516	deletion
-	Ser 517	deletion
-	Arg 518	deletion
-	Thr 519	deletion
-	Ser 520	deletion
-	Met 521	deletion
-	Arg 522	deletion
-	Pro 523	deletion
-	Arg 524	deletion
-	Ser 525	deletion
-	Ser 526	deletion
-	Arg 527	deletion
-	Gly 528	deletion
-	Ser 529	deletion
-	Ile 530	deletion
-	Phe 531	deletion
-	Thr 532	deletion
-	Phe 533	deletion
-	Arg 534	deletion
-	Arg 535	deletion
-	Arg 536	deletion
-	Asp 537	deletion
-	Gln 538	deletion
-	Gly 539	deletion
-	Ser 540	deletion
-	Glu 541	deletion
-	Ala 542	deletion
-	Asp 543	deletion
-	Phe 544	deletion
-	Ala 545	deletion
-	Asp 546	deletion
-	Asp 547	deletion
-	Glu 548	deletion
-	Asn 549	deletion
-	Ser 550	deletion
-	Thr 551	deletion
-	Ala 552	deletion
-	Gly 553	deletion
-	Glu 554	deletion
-	Ser 555	deletion
-	Glu 556	deletion
-	Ser 557	deletion
-	His 558	deletion
-	Arg 559	deletion
-	Thr 560	deletion
-	Ser 561	deletion
-	Leu 562	deletion
-	Leu 563	deletion
-	Val 564	deletion
-	Pro 565	deletion
-	Trp 566	deletion
-	Pro 567	deletion
-	Leu 568	deletion
-	Arg 569	deletion
-	His 570	deletion
-	Pro 571	deletion
-	Ser 572	deletion
-	Ala 573	deletion
-	Gln 574	deletion
-	Gly 575	deletion
-	Gln 576	deletion
-	Pro 577	deletion
-	Gly 578	deletion
-	Pro 579	deletion
-	Gly 580	deletion
-	Ala 581	deletion
-	Ser 582	deletion
-	Ala 583	deletion
-	Pro 584	deletion
-	Gly 585	deletion
-	Tyr 586	deletion
-	Val 587	deletion
-	Leu 588	deletion
-	Asn 589	deletion
-	Gly 590	deletion
-	Lys 591	deletion
-	Arg 592	deletion
-	Asn 593	deletion
-	Ser 594	deletion
-	Thr 595	deletion
-	Val 596	deletion
-	Asp 597	deletion
-	Cys 598	deletion
-	Asn 599	deletion
-	Gly 600	deletion
-	Val 601	deletion
-	Val 602	deletion
-	Ser 603	deletion
-	Leu 604	deletion
-	Leu 605	deletion
-	Gly 606	deletion
-	Ala 607	deletion
-	Gly 608	deletion
-	Asp 609	deletion
-	Ala 610	deletion
-	Glu 611	deletion
-	Ala 612	deletion
-	Thr 613	deletion
-	Ser 614	deletion
-	Pro 615	deletion
-	Gly 616	deletion
-	Ser 617	deletion
-	Tyr 618	deletion
-	Leu 619	deletion
-	Leu 620	deletion
-	Arg 621	deletion
-	Pro 622	deletion
-	Met 623	deletion
-	Val 624	deletion
-	Leu 625	deletion
-	Asp 626	deletion
-	Arg 627	deletion
-	Pro 628	deletion
-	Pro 629	deletion
-	Asp 630	deletion
-	Thr 631	deletion
-	Thr 632	deletion
-	Thr 633	deletion
-	Pro 634	deletion
-	Ser 635	deletion
-	Glu 636	deletion
-	Glu 637	deletion
-	Pro 638	deletion
-	Gly 639	deletion
-	Gly 640	deletion
-	Pro 641	deletion
-	Gln 642	deletion
-	Met 643	deletion
-	Leu 644	deletion
-	Thr 645	deletion
-	Pro 646	deletion
-	Gln 647	deletion
-	Ala 648	deletion
-	Pro 649	deletion
-	Cys 650	deletion
-	Ala 651	deletion
-	Asp 652	deletion
-	Gly 653	deletion
-	Phe 654	deletion
-	Glu 655	deletion
-	Glu 656	deletion
-	Pro 657	deletion
-	Gly 658	deletion
-	Ala 659	deletion
-	Leu 1070	deletion
-	Gly 1071	deletion
-	Thr 1072	deletion
-	Glu 1073	deletion
-	Glu 1074	deletion
-	Glu 1075	deletion
-	Ser 1076	deletion
-	Ser 1077	deletion
-	Lys 1078	deletion
-	Gln 1079	deletion
-	Glu 1080	deletion
-	Ser 1081	deletion
-	Gln 1082	deletion
-	Val 1083	deletion
-	Val 1084	deletion
-	Ser 1085	deletion
-	Gly 1086	deletion
-	Gly 1087	deletion
-	His 1088	deletion
-	Glu 1089	deletion
-	Pro 1090	deletion
-	Tyr 1091	deletion
-	Gln 1092	deletion
-	Glu 1093	deletion
-	Pro 1094	deletion
-	Arg 1095	deletion
-	Ala 1096	deletion
-	Trp 1097	deletion
-	Ser 1098	deletion
-	Gln 1099	deletion
-	Val 1100	deletion
-	Ser 1101	deletion
-	Glu 1102	deletion
-	Thr 1103	deletion
-	Thr 1104	deletion
-	Ser 1105	deletion
-	Ser 1106	deletion
-	Glu 1107	deletion
-	Ala 1108	deletion
-	Gly 1109	deletion
-	Ala 1110	deletion
-	Ser 1111	deletion
-	Thr 1112	deletion
-	Ser 1113	deletion
-	Gln 1114	deletion
-	Ala 1115	deletion
-	Asp 1116	deletion
-	Trp 1117	deletion
-	Gln 1118	deletion
-	Gln 1119	deletion
-	Glu 1120	deletion
-	Gln 1121	deletion
-	Lys 1122	deletion
-	Thr 1123	deletion
-	Glu 1124	deletion
-	Pro 1125	deletion
-	Gln 1126	deletion
-	Ala 1127	deletion
-	Pro 1128	deletion
-	Gly 1129	deletion
-	Cys 1130	deletion
-	Gly 1131	deletion
-	Glu 1132	deletion
-	Thr 1133	deletion
-	Pro 1134	deletion
-	Glu 1135	deletion
-	Asp 1136	deletion
-	Ser 1137	deletion
-	Tyr 1138	deletion
-	Ser 1139	deletion
-	Glu 1140	deletion
-	Gly 1141	deletion
-	Ser 1142	deletion
-	Thr 1143	deletion
-	Ala 1144	deletion
-	Asp 1145	deletion
-	Met 1146	deletion
-	Thr 1147	deletion
-	Asn 1148	deletion
-	Thr 1149	deletion
-	Ala 1150	deletion
-	Asp 1151	deletion
-	Leu 1152	deletion
-	Leu 1153	deletion
-	Glu 1154	deletion
-	Gln 1155	deletion
-	Ile 1156	deletion
-	Pro 1157	deletion
-	Asp 1158	deletion
-	Leu 1159	deletion
-	Gly 1160	deletion
-	Glu 1161	deletion
-	Asp 1162	deletion
-	Val 1163	deletion
-	Lys 1164	deletion
-	Asp 1165	deletion
-	Pro 1166	deletion
-	Glu 1167	deletion
-	Asp 1168	deletion
-	Cys 1169	deletion
-	Phe 1170	deletion
-	Thr 1171	deletion
-	Glu 1172	deletion
-	Gly 1173	deletion
-	Cys 1174	deletion
-	Val 1175	deletion
-	Arg 1176	deletion
-	Arg 1177	deletion
-	Cys 1178	deletion
-	Pro 1179	deletion
-	Cys 1180	deletion
-	Cys 1181	deletion
-	Met 1182	deletion
-	Val 1183	deletion
-	Asp 1184	deletion
-	Thr 1185	deletion
-	Thr 1186	deletion
-	Gln 1187	deletion
-	Ser 1188	deletion
-	Pro 1189	deletion
Val 1932	-	linker
Asp 1933	-	linker
Leu 1934	-	linker
Glu 1935	-	linker
Val 1936	-	linker
Leu 1937	-	linker
Phe 1938	-	linker
Gln 1939	-	linker
Gly 1940	-	linker
Pro 1941	-	linker
Gly 1942	-	linker
Ser 1943	-	linker
Met 1944	-	linker
Val 1945	-	linker

A: 1946 - 2182 (UniProt: P42212)

PDB	External Database	Details
Leu 2008	Phe 64	conflict
Thr 2009	Ser 65	conflict
Leu 2175	His 231	conflict
Gly 2183	-	expression tag
Ser 2184	-	expression tag
Asp 2185	-	expression tag
Tyr 2186	-	expression tag
Lys 2187	-	expression tag
Asp 2188	-	expression tag
Asp 2189	-	expression tag
Asp 2190	-	expression tag
Asp 2191	-	expression tag
Lys 2192	-	expression tag

Contents of the asymmetric unit

Polymers	Number of chains	1
	Total formula weight	213523.9
Branched	Number of molecules	4
	Total formula weight	2508.3
Non-Polymers*	Number of molecules	28
	Total formula weight	15751.3
All*	Total formula weight	231783.5

*Water molecules are not included.