6JP5: Rabbit Cav1.1-Nifedipine Complex
Rabbit Cav1.1-Nifedipine Complex. Determined by electron microscopy at 2.9 Å resolution. Released 12 Jun 2019.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organism
- Oryctolagus cuniculus
- Chains
- 5
- Atoms
- 22,068
- Mol. weight
- 470.87 kDa
- Ligands
- 3PE, CA, NAG, ETA
- Released
- 12 Jun 2019
Explore 6JP5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6JP5 contains 135 α-helices and 88 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 77 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-48 | 4 | |
| α-helix | 53-69 | 17 | |
| α-helix | 75-77 | 3 | |
| α-helix | 89-100 | 12 | |
| α-helix | 112-119 | 8 | |
| α-helix | 121-143 | 23 | |
| α-helix | 166-175 | 10 | |
| α-helix | 180-191 | 12 | |
| α-helix | 197-218 | 22 | |
| β-strand | 225 | 1 | 1 |
| β-strand | 226-228 | 3 | 2 |
| β-strand | 234 | 1 | 2 |
| α-helix | 240-242 | 3 | |
| β-strand | 244 | 1 | 1 |
| β-strand | 259-261 | 3 | 2 |
| α-helix | 278-289 | 12 | |
| α-helix | 294-305 | 12 | |
| α-helix | 311-317 | 7 | |
| α-helix | 318-324 | 7 | |
| α-helix | 325-344 | 20 | |
| α-helix | 345-349 | 5 | |
| α-helix | 350-371 | 22 | |
| α-helix | 420-430 | 11 | |
| α-helix | 432-435 | 4 | |
| α-helix | 439-450 | 12 | |
| α-helix | 458-485 | 28 | |
| α-helix | 488-493 | 6 | |
| α-helix | 497-513 | 17 | |
| α-helix | 514-516 | 3 | |
| α-helix | 523-526 | 4 | |
| α-helix | 530-532 | 3 | |
| α-helix | 534-541 | 8 | |
| α-helix | 548-554 | 7 | |
| α-helix | 558-581 | 24 | |
| α-helix | 600-611 | 12 | |
| α-helix | 616-626 | 11 | |
| α-helix | 637-646 | 10 | |
| α-helix | 651-652 | 2 | |
| α-helix | 653-657 | 5 | |
| α-helix | 658-662 | 5 | |
| α-helix | 666-676 | 11 | |
| α-helix | 679-686 | 8 | |
| α-helix | 789-797 | 9 | |
| α-helix | 799-805 | 7 | |
| α-helix | 809-815 | 7 | |
| α-helix | 827-831 | 5 | |
| α-helix | 833-853 | 21 | |
| α-helix | 870-882 | 13 | |
| α-helix | 893-898 | 6 | |
| α-helix | 903-910 | 8 | |
| α-helix | 912-923 | 12 | |
| α-helix | 931-950 | 20 | |
| β-strand | 955 | 1 | 3 |
| β-strand | 971-975 | 5 | 4 |
| α-helix | 976-978 | 3 | |
| β-strand | 983-987 | 5 | 4 |
| β-strand | 992 | 1 | 3 |
| α-helix | 1000-1011 | 12 | |
| α-helix | 1016-1024 | 9 | |
| α-helix | 1039-1041 | 3 | |
| α-helix | 1042-1049 | 8 | |
| α-helix | 1050-1056 | 7 | |
| α-helix | 1058-1069 | 12 | |
| α-helix | 1083-1094 | 12 | |
| α-helix | 1106-1115 | 10 | |
| α-helix | 1118-1124 | 7 | |
| α-helix | 1128-1136 | 9 | |
| α-helix | 1144-1172 | 29 | |
| α-helix | 1181-1205 | 25 | |
| α-helix | 1233-1238 | 6 | |
| α-helix | 1241-1247 | 7 | |
| α-helix | 1251-1265 | 15 | |
| α-helix | 1268-1288 | 21 | |
| β-strand | 1292 | 1 | 5 |
| β-strand | 1296 | 1 | 6 |
| β-strand | 1298 | 1 | 6 |
| α-helix | 1309-1321 | 13 | |
| α-helix | 1325-1331 | 7 | |
| α-helix | 1336-1337 | 2 | |
| β-strand | 1338 | 1 | 5 |
| α-helix | 1339 | 1 | |
| α-helix | 1357-1380 | 24 | |
| α-helix | 1384-1387 | 4 | |
| α-helix | 1396-1406 | 11 | |
| β-strand | 1416-1417 | 2 | 7 |
| α-helix | 1423-1426 | 4 | |
| α-helix | 1443-1450 | 8 | |
| β-strand | 1461-1462 | 2 | 7 |
| α-helix | 1463-1474 | 12 | |
| α-helix | 1483-1492 | 10 | |
| α-helix | 1495-1496 | 2 | |
| α-helix | 1501-1505 | 5 | |
Chain B: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 79-94 | 16 | |
| α-helix | 100-101 | 2 | |
| β-strand | 103-107 | 5 | 27 |
| β-strand | 111 | 1 | 28 |
| β-strand | 125 | 1 | 27 |
| β-strand | 128 | 1 | 28 |
| β-strand | 133-139 | 7 | 27 |
| β-strand | 144-149 | 6 | 27 |
| β-strand | 156-160 | 5 | 27 |
| α-helix | 161 | 1 | |
| α-helix | 162-170 | 9 | |
Chain C: 9 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 268-271 | 4 | 27 |
| α-helix | 275 | 1 | |
| β-strand | 276-280 | 5 | 29 |
| α-helix | 288-303 | 16 | |
| β-strand | 309-313 | 5 | 29 |
| α-helix | 344-356 | 13 | |
| β-strand | 363-367 | 5 | 29 |
| α-helix | 375-377 | 3 | |
| β-strand | 385-389 | 5 | 29 |
| α-helix | 394-401 | 8 | |
| α-helix | 408-410 | 3 | |
| α-helix | 412-424 | 13 | |
| α-helix | 427-429 | 3 | |
| β-strand | 432-434 | 3 | 29 |
| α-helix | 439-457 | 19 | |
Chain E: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-26 | 19 | |
| β-strand | 48-50 | 3 | 8 |
| β-strand | 56-59 | 4 | 8 |
| β-strand | 79-81 | 3 | 8 |
| α-helix | 105-127 | 23 | |
| α-helix | 137-164 | 28 | |
| α-helix | 182-201 | 20 | |
Chain F: 41 helices, 57 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-37 | 8 | |
| α-helix | 42-52 | 11 | |
| α-helix | 54-64 | 11 | |
| β-strand | 68-72 | 5 | 9 |
| α-helix | 77-108 | 32 | |
| β-strand | 124-125 | 2 | 10 |
| β-strand | 127-128 | 2 | 11 |
| β-strand | 144-145 | 2 | 10 |
| β-strand | 152 | 1 | 12 |
| β-strand | 161 | 1 | 12 |
| β-strand | 162 | 1 | 13 |
| β-strand | 167-169 | 3 | 11 |
| β-strand | 176 | 1 | 14 |
| β-strand | 178 | 1 | 14 |
| α-helix | 179-187 | 9 | |
| α-helix | 188-191 | 4 | |
| α-helix | 192-201 | 10 | |
| β-strand | 208-212 | 5 | 11 |
| β-strand | 217-220 | 4 | 11 |
| β-strand | 222 | 1 | 13 |
| α-helix | 244-250 | 7 | |
| β-strand | 254-261 | 8 | 15 |
| α-helix | 264-266 | 3 | |
| α-helix | 269-283 | 15 | |
| β-strand | 290-296 | 7 | 15 |
| β-strand | 300-302 | 3 | 15 |
| β-strand | 310 | 1 | 15 |
| α-helix | 314-323 | 10 | |
| α-helix | 335-346 | 12 | |
| β-strand | 357-364 | 8 | 15 |
| α-helix | 372-378 | 7 | |
| β-strand | 385-391 | 7 | 15 |
| α-helix | 399-407 | 9 | |
| β-strand | 411-415 | 5 | 15 |
| α-helix | 418-420 | 3 | |
| α-helix | 429-432 | 4 | |
| α-helix | 434-437 | 4 | |
| α-helix | 440-443 | 4 | |
| β-strand | 447-448 | 2 | 11 |
| α-helix | 449-451 | 3 | |
| β-strand | 452-453 | 2 | 11 |
| β-strand | 460-469 | 10 | 11 |
| β-strand | 486-495 | 10 | 11 |
| α-helix | 496-499 | 4 | |
| β-strand | 513-517 | 5 | 16 |
| β-strand | 522 | 1 | 17 |
| β-strand | 523-525 | 3 | 16 |
| α-helix | 533-534 | 2 | |
| α-helix | 543-545 | 3 | |
| β-strand | 562 | 1 | 17 |
| α-helix | 563-566 | 4 | |
| α-helix | 574-579 | 6 | |
| β-strand | 586-595 | 10 | 16 |
| α-helix | 596 | 1 | |
| β-strand | 602-613 | 12 | 16 |
| β-strand | 621-627 | 7 | 16 |
| β-strand | 632-636 | 5 | 9 |
| α-helix | 641-646 | 6 | |
| α-helix | 653-655 | 3 | |
| β-strand | 661-662 | 2 | 18 |
| β-strand | 670 | 1 | 19 |
| α-helix | 679-692 | 14 | |
| β-strand | 700 | 1 | 19 |
| α-helix | 702-712 | 11 | |
| α-helix | 714-718 | 5 | |
| α-helix | 719-723 | 5 | |
| β-strand | 732-734 | 3 | 20 |
| β-strand | 737-739 | 3 | 20 |
| β-strand | 745-746 | 2 | 18 |
| α-helix | 751-753 | 3 | |
| α-helix | 765-772 | 8 | |
| β-strand | 776 | 1 | 21 |
| β-strand | 777-779 | 3 | 20 |
| α-helix | 780-782 | 3 | |
| β-strand | 796-800 | 5 | 20 |
| β-strand | 803-804 | 2 | 22 |
| β-strand | 809-810 | 2 | 22 |
| β-strand | 813-819 | 7 | 20 |
| α-helix | 820 | 1 | |
| α-helix | 821-829 | 9 | |
| β-strand | 851-856 | 6 | 23 |
| β-strand | 861 | 1 | 24 |
| β-strand | 862-865 | 4 | 23 |
| β-strand | 877 | 1 | 24 |
| α-helix | 878-880 | 3 | |
| α-helix | 883-891 | 9 | |
| β-strand | 896-907 | 12 | 25 |
| β-strand | 975-985 | 11 | 25 |
| β-strand | 992-994 | 3 | 23 |
| β-strand | 997-998 | 2 | 26 |
| β-strand | 1003-1004 | 2 | 26 |
| β-strand | 1007-1010 | 4 | 23 |
| β-strand | 1014 | 1 | 21 |
| β-strand | 1017-1022 | 6 | 23 |
| α-helix | 1024-1026 | 3 | |
| β-strand | 1039-1040 | 2 | 25 |
| α-helix | 1046-1049 | 4 | |
| α-helix | 1053-1055 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Voltage-dependent L-type calcium channel subunit alpha-1S | A | protein | 1873 | Oryctolagus cuniculus | P07293 (AlphaFold model) |
| Voltage-dependent calcium channel gamma-1 subunit | E | protein | 222 | Oryctolagus cuniculus | P19518 (AlphaFold model) |
| Voltage-dependent calcium channel subunit alpha-2/delta-1 | F | protein | 1073 | Oryctolagus cuniculus | P13806 (AlphaFold model) |
| Voltage-dependent L-type calcium channel subunit beta-1 | B, C | protein | 450 | Oryctolagus cuniculus | P19517 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>6JP5_1 Voltage-dependent L-type calcium channel subunit alpha-1S (chains A)
MEPSSPQDEGLRKKQPKKPLPEVLPRPPRALFCLTLQNPLRKACISIVEWKPFETIILLT
IFANCVALAVYLPMPEDDNNSLNLGLEKLEYFFLTVFSIEAAMKIIAYGFLFHQDAYLRS
GWNVLDFIIVFLGVFTAILEQVNVIQSNTAPMSSKGAGLDVKALRAFRVLRPLRLVSGVP
SLQVVLNSIFKAMLPLFHIALLVLFMVIIYAIIGLELFKGKMHKTCYYIGTDIVATVENE
KPSPCARTGSGRPCTINGSECRGGWPGPNHGITHFDNFGFSMLTVYQCITMEGWTDVLYW
VNDAIGNEWPWIYFVTLILLGSFFILNLVLGVLSGEFTKEREKAKSRGTFQKLREKQQLE
EDLRGYMSWITQGEVMDVEDLREGKLSLEEGGSDTESLYEIEGLNKIIQFIRHWRQWNRV
FRWKCHDLVKSRVFYWLVILIVALNTLSIASEHHNQPLWLTHLQDIANRVLLSLFTIEML
LKMYGLGLRQYFMSIFNRFDCFVVCSGILELLLVESGAMTPLGISVLRCIRLLRLFKITK
YWTSLSNLVASLLNSIRSIASLLLLLFLFIIIFALLGMQLFGGRYDFEDTEVRRSNFDNF
PQALISVFQVLTGEDWNSVMYNGIMAYGGPSYPGVLVCIYFIILFVCGNYILLNVFLAIA
VDNLAEAESLTSAQKAKAEERKRRKMSRGLPDKTEEEKSVMAKKLEQKPKGEGIPTTAKL
KVDEFESNVNEVKDPYPSADFPGDDEEDEPEIPVSPRPRPLAELQLKEKAVPIPEASSFF
IFSPTNKVRVLCHRIVNATWFTNFILLFILLSSAALAAEDPIRAESVRNQILGYFDIAFT
SVFTVEIVLKMTTYGAFLHKGSFCRNYFNILDLLVVAVSLISMGLESSTISVVKILRVLR
VLRPLRAINRAKGLKHVVQCVFVAIRTIGNIVLVTTLLQFMFACIGVQLFKGKFFSCNDL
SKMTEEECRGYYYVYKDGDPTQMELRPRQWIHNDFHFDNVLSAMMSLFTVSTFEGWPQLL
YRAIDSNEEDMGPVYNNRVEMAIFFIIYIILIAFFMMNIFVGFVIVTFQEQGETEYKNCE
LDKNQRQCVQYALKARPLRCYIPKNPYQYQVWYVVTSSYFEYLMFALIMLNTICLGMQHY
HQSEEMNHISDILNVAFTIIFTLEMILKLLAFKARGYFGDPWNVFDFLIVIGSIIDVILS
EIDTFLASSGGLYCLGGGCGNVDPDESARISSAFFRLFRVMRLIKLLSRAEGVRTLLWTF
IKSFQALPYVALLIVMLFFIYAVIGMQMFGKIALVDGTQINRNNNFQTFPQAVLLLFRCA
TGEAWQEILLACSYGKLCDPESDYAPGEEYTCGTNFAYYYFISFYMLCAFLIINLFVAVI
MDNFDYLTRDWSILGPHHLDEFKAIWAEYDPEAKGRIKHLDVVTLLRRIQPPLGFGKFCP
HRVACKRLVGMNMPLNSDGTVTFNATLFALVRTALKIKTEGNFEQANEELRAIIKKIWKR
TSMKLLDQVIPPIGDDEVTVGKFYATFLIQEHFRKFMKRQEEYYGYRPKKDTVQIQAGLR
TIEEEAAPEIRRTISGDLTAEEELERAMVEAAMEERIFRRTGGLFGQVDTFLERTNSLPP
VMANQRPLQFAEIEMEELESPVFLEDFPQDARTNPLARANTNNANANVAYGNSNHSNNQM
FSSVHCEREFPGEAETPAAGRGALSHSHRALGPHSKPCAGKLNGQLVQPGMPINQAPPAP
CQQPSTDPPERGQRRTSLTGSLQDEAPQRRSSEGSTPRRPAPATALLIQEALVRGGLDTL
AADAGFVTATSQALADACQMEPEEVEVAATELLKARESVQGMASVPGSLSRRSSLGSLDQ
VQGSQETLIPPRP
Sequence of entity 2 (E), FASTA
>6JP5_2 Voltage-dependent calcium channel gamma-1 subunit (chains E)
MSPTEAPKVRVTLFCILVGIVLAMTAVVSDHWAVLSPHMENHNTTCEAAHFGLWRICTKR
IALGEDRSCGPITLPGEKNCSYFRHFNPGESSEIFEFTTQKEYSISAAAISVFSLGFLIM
GTICALMAFRKKRDYLLRPASMFYVFAGLCLFVSLEVMRQSVKRMIDSEDTVWIEYYYSW
SFACACAAFVLLFLGGISLLLFSLPRMPQNPWESCMDAEPEH
Sequence of entity 3 (F), FASTA
>6JP5_3 Voltage-dependent calcium channel subunit alpha-2/delta-1 (chains F)
MAAGRPLAWTLTLWQAWLILIGPSSEEPFPSAVTIKSWVDKMQEDLVTLAKTASGVHQLV
DIYEKYQDLYTVEPNNARQLVEIAARDIEKLLSNRSKALVRLALEAEKVQAAHQWREDFA
SNEVVYYNAKDDLDPEKNDSEPGSQRIKPVFIDDANFRRQVSYQHAAVHIPTDIYEGSTI
VLNELNWTSALDDVFKKNREEDPSLLWQVFGSATGLARYYPASPWVDNSRTPNKIDLYDV
RRRPWYIQGAASPKDMLILVDVSGSVSGLTLKLIRTSVSEMLETLSDDDFVNVASFNSNA
QDVSCFQHLVQANVRNKKVLKDAVNNITAKGITDYKKGFSFAFEQLLNYNVSRANCNKII
MLFTDGGEERAQEIFAKYNKDKKVRVFTFSVGQHNYDRGPIQWMACENKGYYYEIPSIGA
IRINTQEYLDVLGRPMVLAGDKAKQVQWTNVYLDALELGLVITGTLPVFNITGQFENKTN
LKNQLILGVMGVDVSLEDIKRLTPRFTLCPNGYYFAIDPNGYVLLHPNLQPKPIGVGIPT
INLRKRRPNVQNPKSQEPVTLDFLDAELENDIKVEIRNKMIDGESGEKTFRTLVKSQDER
YIDKGNRTYTWTPVNGTDYSLALVLPTYSFYYIKAKIEETITQARYSETLKPDNFEESGY
TFLAPRDYCSDLKPSDNNTEFLLNFNEFIDRKTPNNPSCNTDLINRVLLDAGFTNELVQN
YWSKQKNIKGVKARFVVTDGGITRVYPKEAGENWQENPETYEDSFYKRSLDNDNYVFTAP
YFNKSGPGAYESGIMVSKAVEIYIQGKLLKPAVVGIKIDVNSWIENFTKTSIRDPCAGPV
CDCKRNSDVMDCVILDDGGFLLMANHDDYTNQIGRFFGEIDPSLMRHLVNISVYAFNKSY
DYQSVCEPGAAPKQGAGHRSAYVPSIADILQIGWWATAAAWSILQQFLLSLTFPRLLEAA
DMEDDDFTASMSKQSCITEQTQYFFDNDSKSFSGVLDCGNCSRIFHVEKLMNTNLIFIMV
ESKGTCPCDTRLLIQAEQTSDGPDPCDMVKQPRYRKGPDVCFDNNVLEDYTDC
Sequence of entity 4 (B, C), FASTA
>6JP5_4 Voltage-dependent L-type calcium channel subunit beta-1 (chains B, C)
QGPHMALRKEAERQALAQLEKAKTKPVAFAVRTNVGYNPSPGDEVPVEGVAITFEPKDFL
HIKEKYNNDWWIGRLVKEGCEVGFIPSPVKLDSLRLLQEQKLRQSRLSSSKSGDNSSSSL
GDVVTGTRRPTPPASGNEMTNLAFELEPLDLEEDEAELGEQSGSAKTSVSSVTTPPPHGT
RIPFFKKTEHVPPYDVVPSMRPIILVGPSLKGYEVTDMMQKALFDFLKHLFDGRISITRV
TADISLAKRSVLNNPSKHIIIERSNTRSSLAEVQSEIERIFELARTLQLVALDADTINHP
AQLSKTSLAPIIVYIKITSPKVLQRLIKSRGKSQSKHLNVQIAASEKLAQCPPEMFDIIL
DENQLEDACEHLAEYLEAYWKATHPPSSTPPNPLLNRTMATAALAASPAPVSNLQVQVLT
SLRRNLSFWGGLETSQRGGGAVPQQQEHAM
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| 3PE | 1,2-Distearoyl-sn-glycerophosphoethanolamine | C41 H82 N O8 P | 8 |
| CA | Calcium ion | Ca | 3 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 9 |
| ETA | Ethanolamine | C2 H7 N O | 1 |
| PC1 | 1,2-diacyl-sn-glycero-3-phosphocholine | C44 H88 N O8 P | 1 |
| C5U | dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate | C17 H18 N2 O6 | 1 |
Primary citation
Molecular Basis for Ligand Modulation of a Mammalian Voltage-Gated Ca2+Channel. Zhao, Y., Huang, G., Wu, J. et al. Cell (2019) 177:1495-1506.e12. DOI 10.1016/j.cell.2019.04.043 · PubMed
Other PDB entries of the same protein (UniProt P07293 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7RXQ 2.03 Å, Crystal structure of junctophilin-2 in complex with a CaV1.1 peptide
- 1T3L 2.2 Å, Structural Analysis of the Voltage-Dependent Calcium Channel Beta Subunit Functional…
- 6JPA 2.6 Å, Rabbit Cav1.1-Verapamil Complex
- 6JP8 2.7 Å, Rabbit Cav1.1-Bay K8644 Complex
- 8E56 2.8 Å, Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone at 2.8…
- 8E57 2.8 Å, Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone and 100…
- 6JPB 2.9 Å, Rabbit Cav1.1-Diltiazem Complex
- 7JPX 2.9 Å, Rabbit Cav1.1 in the presence of 100 micromolar amlodipine in nanodiscs at 2.9 Angstrom…
- 7JPK 3.0 Å, Rabbit Cav1.1 in the presence of 100 micromolar (S)-(-)-Bay K8644 in nanodiscs at 3.0…
- 8E58 3.0 Å, Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone and 1…
- 7JPW 3.2 Å, Rabbit Cav1.1 in the presence of 100 micromolar (R)-(+)-Bay K8644 in nanodiscs at 3.2…
- 7JPL 3.4 Å, Rabbit Cav1.1 in the presence of 10 micromolar (S)-(-)-Bay K8644 in nanodiscs at 3.4…
Browse structure collections
About this viewer
MolViewer shows 6JP5 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.