9H9P: CDK5 regulatory subunit-associated protein 2
Spokes 12 and 13 of the human gamma-tubulin ring complex in complex with CDK5RAP2 and docked MZT2/GCP2-NHD module. Determined by electron microscopy at 4.5 Å resolution. Released 15 Jan 2025.
- Method
- Electron microscopy
- Resolution
- 4.5 Å
- Organism
- Homo sapiens
- Chains
- 7
- Atoms
- 16,352
- Mol. weight
- 856.97 kDa
- Ligands
- GDP
- Released
- 15 Jan 2025
Explore 9H9P in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9H9P contains 101 α-helices and 48 β-strands across 7 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: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 62-91 | 30 | |
Chain C: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-47 | 13 | |
| α-helix | 53-64 | 12 | |
| α-helix | 69-79 | 11 | |
Chain G: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 62-89 | 28 | |
Chain l: 18 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 5 |
| α-helix | 11-28 | 18 | |
| β-strand | 31 | 1 | 6 |
| β-strand | 37 | 1 | 6 |
| β-strand | 52-53 | 2 | 7 |
| β-strand | 61-62 | 2 | 7 |
| β-strand | 64-66 | 3 | 5 |
| α-helix | 73-79 | 7 | |
| α-helix | 81-84 | 4 | |
| α-helix | 104-128 | 25 | |
| β-strand | 132-138 | 7 | 5 |
| β-strand | 140 | 1 | 8 |
| α-helix | 145-160 | 16 | |
| β-strand | 167-168 | 2 | 5 |
| β-strand | 171-172 | 2 | 8 |
| α-helix | 184-198 | 15 | |
| β-strand | 201-202 | 2 | 5 |
| β-strand | 203 | 1 | 9 |
| β-strand | 205-206 | 2 | 8 |
| α-helix | 207-213 | 7 | |
| α-helix | 214-218 | 5 | |
| α-helix | 225-239 | 15 | |
| α-helix | 241-244 | 4 | |
| α-helix | 253-260 | 8 | |
| β-strand | 263 | 1 | 10 |
| β-strand | 266 | 1 | 10 |
| β-strand | 269 | 1 | 9 |
| β-strand | 270-272 | 3 | 11 |
| α-helix | 290-296 | 7 | |
| β-strand | 317-324 | 8 | 11 |
| α-helix | 330-332 | 3 | |
| α-helix | 333-343 | 11 | |
| β-strand | 348 | 1 | 11 |
| β-strand | 356-360 | 5 | 11 |
| α-helix | 362-364 | 3 | |
| β-strand | 376-381 | 6 | 11 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-399 | 15 | |
| α-helix | 420-437 | 18 | |
Chain L: 25 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 353-357 | 5 | |
| α-helix | 393-413 | 21 | |
| α-helix | 427-446 | 20 | |
| α-helix | 456-462 | 7 | |
| α-helix | 464-476 | 13 | |
| α-helix | 499-511 | 13 | |
| α-helix | 518-528 | 11 | |
| α-helix | 530-537 | 8 | |
| α-helix | 538-542 | 5 | |
| α-helix | 589-606 | 18 | |
| α-helix | 1478-1481 | 4 | |
| α-helix | 1485-1502 | 18 | |
| α-helix | 1505-1515 | 11 | |
| α-helix | 1524-1534 | 11 | |
| α-helix | 1547-1561 | 15 | |
| β-strand | 1573 | 1 | 1 |
| β-strand | 1597 | 1 | 1 |
| α-helix | 1602-1605 | 4 | |
| α-helix | 1610-1641 | 32 | |
| α-helix | 1653-1677 | 25 | |
| α-helix | 1678-1682 | 5 | |
| α-helix | 1683-1686 | 4 | |
| α-helix | 1699-1715 | 17 | |
| α-helix | 1720-1722 | 3 | |
| α-helix | 1723-1741 | 19 | |
| α-helix | 1762-1786 | 25 | |
| α-helix | 1793-1802 | 10 | |
Chain m: 16 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 12 |
| α-helix | 11-28 | 18 | |
| β-strand | 31 | 1 | 13 |
| β-strand | 37 | 1 | 13 |
| β-strand | 53 | 1 | 14 |
| β-strand | 61 | 1 | 14 |
| β-strand | 64-65 | 2 | 12 |
| α-helix | 73-79 | 7 | |
| α-helix | 81-85 | 5 | |
| α-helix | 104-113 | 10 | |
| α-helix | 115-126 | 12 | |
| β-strand | 132-140 | 9 | 12 |
| α-helix | 145-160 | 16 | |
| β-strand | 165-171 | 7 | 12 |
| β-strand | 172 | 1 | 15 |
| α-helix | 184-198 | 15 | |
| β-strand | 201-203 | 3 | 12 |
| β-strand | 206 | 1 | 15 |
| α-helix | 207-216 | 10 | |
| α-helix | 225-239 | 15 | |
| α-helix | 241-244 | 4 | |
| α-helix | 255-258 | 4 | |
| β-strand | 268-269 | 2 | 12 |
| β-strand | 273 | 1 | 16 |
| α-helix | 290-297 | 8 | |
| β-strand | 317 | 1 | 17 |
| β-strand | 320-324 | 5 | 16 |
| α-helix | 332-343 | 12 | |
| β-strand | 348 | 1 | 17 |
| β-strand | 356-360 | 5 | 16 |
| β-strand | 376-378 | 3 | 16 |
| β-strand | 381 | 1 | 17 |
| α-helix | 382-384 | 3 | |
| α-helix | 385-401 | 17 | |
| α-helix | 420-437 | 18 | |
Chain M: 37 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-16 | 11 | |
| α-helix | 25-33 | 9 | |
| α-helix | 47-53 | 7 | |
| α-helix | 61-72 | 12 | |
| α-helix | 79-90 | 12 | |
| α-helix | 92-106 | 15 | |
| α-helix | 233-235 | 3 | |
| α-helix | 241-252 | 12 | |
| α-helix | 256-258 | 3 | |
| β-strand | 262-264 | 3 | 2 |
| β-strand | 273-275 | 3 | 2 |
| α-helix | 282-307 | 26 | |
| α-helix | 315-323 | 9 | |
| α-helix | 325-342 | 18 | |
| α-helix | 349-375 | 27 | |
| α-helix | 381-393 | 13 | |
| α-helix | 401-411 | 11 | |
| α-helix | 413-424 | 12 | |
| β-strand | 437-439 | 3 | 3 |
| α-helix | 446-449 | 4 | |
| β-strand | 460-462 | 3 | 3 |
| α-helix | 472-474 | 3 | |
| α-helix | 475-489 | 15 | |
| α-helix | 511-533 | 23 | |
| α-helix | 537-548 | 12 | |
| α-helix | 553-567 | 15 | |
| α-helix | 570 | 1 | |
| α-helix | 576-589 | 14 | |
| α-helix | 591-593 | 3 | |
| α-helix | 598-600 | 3 | |
| β-strand | 601-605 | 5 | 4 |
| α-helix | 610-619 | 10 | |
| α-helix | 641-643 | 3 | |
| β-strand | 644-648 | 5 | 4 |
| α-helix | 652-655 | 4 | |
| α-helix | 660-689 | 30 | |
| α-helix | 707-727 | 21 | |
| α-helix | 730-740 | 11 | |
| α-helix | 741-743 | 3 | |
| α-helix | 747-764 | 18 | |
| α-helix | 770-790 | 21 | |
| α-helix | 847-874 | 28 | |
| α-helix | 878-887 | 10 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| CDK5 regulatory subunit-associated protein 2 | A, G | protein | 1893 | Homo sapiens | Q96SN8 (AlphaFold model) |
| Gamma-tubulin complex component 6 | L | protein | 1819 | Homo sapiens | Q96RT7 (AlphaFold model) |
| Isoform 3 of Gamma-tubulin complex component 2 | M | protein | 930 | Homo sapiens | Q9BSJ2 (AlphaFold model) |
| Tubulin gamma-1 chain | l, m | protein | 451 | Homo sapiens | P23258 (AlphaFold model) |
| Mitotic-spindle organizing protein 2A | C | protein | 158 | Homo sapiens | Q6P582 |
Sequence of entity 1 (A, G), FASTA
>9H9P_1 CDK5 regulatory subunit-associated protein 2 (chains A, G)
MMDLVLEEDVTVPGTLSGCSGLVPSVPDDLDGINPNAGLGNGLLPNVSEETVSPTRARNM
KDFENQITELKKENFNLKLRIYFLEERMQQEFHGPTEHIYKTNIELKVEVESLKRELQER
EQLLIKASKAVESLAEAGGSEIQRVKEDARKKVQQVEDLLTKRILLLEKDVTAAQAELEK
AFAGTETEKALRLRLESKLSEMKKMHEGDLAMALVLDEKDRLIEELKLSLKSKEALIQCL
KEEKSQMACPDENVSSGELRGLCAAPREEKERETEAAQMEHQKERNSFQERIQALEEDLR
EKEREIATEKKNSLKRDKAIQGLTMALKSKEKKVEELNSEIEKLSAAFAKAREALQKAQT
QEFQGSEDYETALSGKEALSAALRSQNLTKSTENHRLRRSIKKITQELSDLQQERERLEK
DLEEAHREKSKGDCTIRDLRNEVEKLRNEVNEREKAMENRYKSLLSESNKKLHNQEQVIK
HLTESTNQKDVLLQKFNEKDLEVIQQNCYLMAAEDLELRSEGLITEKCSSQQPPGSKTIF
SKEKKQSSDYEELIQVLKKEQDIYTHLVKSLQESDSINNLQAELNKIFALRKQLEQDVLS
YQNLRKTLEEQISEIRRREEESFSLYSDQTFYLSICLEENNRFQVEHFSQEELKKKVSDL
IQLVKELYTDNQHLKKTIFDLSCMGFQGNGFPDRLASTEQTELLASKEDEDTIKIGEDDE
INFLSDQHLQQSNEIMKDLSKGGCKNGYLRHTESKISDCDGAHAPGCLEEGAFINLLAPL
FNEKATLLLESRPDLLKVVRELLLGQLFLTEQEVSGEHLDGKTEKTPKQKGELVHFVQTN
SFSKPHDELKLSCEAQLVKAGEVPKVGLKDASVQTVATEGDLLRFKHEATREAWEEKPIN
TALSAEHRPENLHGVPGWQAALLSLPGITNREAKKSRLPILIKPSRSLGNMYRLPATQEV
VTQLQSQILELQGELKEFKTCNKQLHQKLILAEAVMEGRPTPDKTLLNAQPPVGAAYQDS
PGEQKGIKTTSSVWRDKEMDSDQQRSYEIDSEICPPDDLASLPSCKENPEDVLSPTSVAT
YLSSKSQPSAKVSVMGTDQSESINTSNETEYLKQKIHDLETELEGYQNFIFQLQKHSQCS
EAIITVLCGTEGAQDGLSKPKNGSDGEEMTFSSLHQVRYVKHVKILGPLAPEMIDSRVLE
NLKQQLEEQEYKLQKEQNLNMQLFSEIHNLQNKFRDLSPPRYDSLVQSQARELSLQRQQI
KDGHGICVISRQHMNTMIKAFEELLQASDVDYCVAEGFQEQLNQCAELLEKLEKLFLNGK
SVGVEMNTQNELMERIEEDNLTYQHLLPESPEPSASHALSDYETSEKSFFSRDQKQDNET
EKTSVMVNSFSQDLLMEHIQEIRTLRKRLEESIKTNEKLRKQLERQGSEFVQGSTSIFAS
GSELHSSLTSEIHFLRKQNQALNAMLIKGSRDKQKENDKLRESLSRKTVSLEHLQREYAS
VKEENERLQKEGSEKERHNQQLIQEVRCSGQELSRVQEELKLRQQLLSQNDKLLQSLRVE
LKAYEKLDEEHRRLREASGEGWKGQDPFRDLHSLLMEIQALRLQLERSIETSSTLQSRLK
EQLARGAEKAQEGALTLAVQAVSIPEVPLQPDKHDGDKYPMESDNSFDLFDSSQAVTPKS
VSETPPLSGNDTDSLSCDSGSSATSTPCVSRLVTGHHLWASKNGRHVLGLIEDYEALLKQ
ISQGQRLLAEMDIQTQEAPSSTSQELGTKGPHPAPLSKFVSSVSTAKLTLEEAYRRLKLL
WRVSLPEDGQCPLHCEQIGEMKAEVTKLHKKLFEQEKKLQNTMKLLQLSKRQEKVIFDQL
VVTHKILRKARGNLELRPGGAHPGTCSPSRPGS
Sequence of entity 2 (L), FASTA
>9H9P_2 Gamma-tubulin complex component 6 (chains L)
MASITQLFDDLCEALLPAAKTHLGQRSVNRKRAKRSLKKVAYNALFTNLFQDETQQLQPD
MSKLPARNKILMLSFDLRVGGLGPKADRLEELVEELEAAPCCPLLEVGSVLDLLVQLAGS
GPPQVLPRKRDYFLNNKHVGRNVPYSGYDCDDLSVFEMDVQSLISREECLCHSMIQETLQ
VMEAAPGTGLPTVGLFSFGDPCGDRFERDTRVSLFGALVHSRTYDMDVRLGLPPVPDNAD
LSGLAIKVPPSVDQWEDEGFQSASNLTPDSQSEPSVTPDVDLWEAALTYEASKRRCWERV
GCPPGHREEPYLTEAGRDAFDKFCRLHQGELQLLAGGVLQAPQPVLVKECELVKDVLNVL
IGVVSATFSLCQPAQAFVVKRGVHVSGASPESISSLLSEVAEYGTCYTRLSHFSLQPVLD
SLYSKGLVFQAFTSGLRRYLQYYRACVLSTPPTLSLLTIGFLFKKLGRQLRYLAELCGVG
AVLPGTCGGGPRAAFPTGVKLLSYLYQEALHNCSNEHYPVLLSLLKTSCEPYTRFIHDWV
YSGVFRDAYGEFMIQVNHEYLSFRDKLYWTHGYVLISKEVEDCVPVFLKHIAHDIYVCGK
TINLLKLCCPRHYLCWSDVPVPRISVIFSLEELKEIEKDCAVYVGRMERVARHSSVSKEE
KELRMEIAKQELIAHAREAASRVLSALSDRQMSERMALDARKREQFQRLKEQFVKDQERR
QAARQEELDDDFSYARELRDRERRLKSLEEELERKARQALVDHYSKLSAEAARREQKALW
RIQRHRLESARLRFLLEDEKHIQEMLKAVSEAHQPQEPPDVLLSVHPQVTSPGPEHPEGG
QGCDSGSAEQHSPAWDGWNRPGLLTPQPLKPLAVGAGGRGLQQAEGARPFSDSLSIGDFL
PVGPGAEPSVQTGMVPLLEVALQTINLDLPPSAPGEAPAAASTQPSRPQEYDFSTVLRPA
VATSPAPGPLQAAECSLGSSGLQLWEDSCGKMDACGSASRETLLPSHPPRRAALEEGSSQ
PTERLFGQVSGGGLPTGDYASEIAPTRPRWNTHGHVSDASIRVGENVSDVAPTQPRWNTH
GHVSNASISLGESVSDVAPTRPRWNIHGHVSNASIRVGENVSDVAPTRPRWNTHGHVSNA
SIRVGENVSDVAPTRPRWNTHGHVSDASISLGESVSDMAPARPRWNTHGHVSDASISLGE
SVSDMAPTRPRWNTHGHVSDTSIRVGENVSDVAPIRSRCNTHGHVSDASISLGEPVSDVV
STRPRWNTHVPIPPPHMVLGALSPEAEPNTPRPQQSPPGHTSQSALSLGAQSTVLDCGPR
LPVEVGPSLSSPSSGCGEGSISVGENVSDVAPTQPWWPNTPGDSVSEELGPGRSGDTEDL
SPNWPLNSQEDTAAQSSPGRGEEAEASAAEAQGGEQAYLAGLAGQYHLERYPDSYESMSE
PPIAHLLRPVLPRAFAFPVDPQVQSAADETAVQLSELLTLPVLMKRSITAPLAAHISLVN
KAAVDYFFVELHLEAHYEALRHFLLMEDGEFAQSLSDLLFEKLGAGQTPGELLNPLVLNS
VLSKALQCSLHGDTPHASNLSLALKYLPEVFAPNAPDVLSCLELRYKVDWPLNIVITEGC
VSKYSGVFSFLLQLKLMMWALKDVCFHLKRTALLSHMAGSVQFRQLQLFKHEMQHFVKVI
QGYIANQILHVTWCEFRARLATVGDLEEIQRAHAEYLHKAVFRGLLTEKAAPVMNVIHSI
FSLVLKFRSQLISQAWGPPGGPRGAEHPNFALMQQSYNTFKYYSHFLFKVVTKLVNRGYQ
PHLEDFLLRINFNNYYQDA
Sequence of entity 3 (M), FASTA
>9H9P_3 Isoform 3 of Gamma-tubulin complex component 2 (chains M)
MSEFRIHHDVNELLSLLRVHGGDGAEVYIDLLQKNRTPYVTTTVSAHSAKVKIAEFSRTP
EDFLKKYDELKSKNTRNLDPLVYLLSKLTEDKETLQYLQQNAKERAELAAAAVGSSTTSI
NVPAAASKISMQELEELRKQLGSVATGSTLQQSLELKRKMLRDKQNKKNSGQHLPIFPAW
VYERPALIGDFLIGAGISTDTALPIVLLRWNLALSPRLKCSGVISAHCNLHLPGTLPLAS
QESAVVEDLLYVLVGVDGRYVSAQPLAGRQSRTFLVDPNLDLSIRELVHRILPVAASYSA
VTRFIEEKSSFEYGQVNHALAAAMRTLVKEHLILVSQLEQLHRQGLLSLQKLWFYIQPAM
RTMDILASLATSVDKGECLGGSTLSLLHDRSFSYTGDSQAQELCLYLTKAASAPYFEVLE
KWIYRGIIHDPYSEFMVEEHELRKERIQEDYNDKYWDQRYTIVQQQIPSFLQKMADKILS
TGKYLNVVRECGHDVTCPVAKEIIYTLKERAYVEQIEKAFNYASKVLLDFLMEEKELVAH
LRSIKRYFLMDQGDFFVHFMDLAEEELRKPVEDITPPRLEALLELALRMSTANTDPFKDD
LKIDLMPHDLITQLLRVLAIETKQEKAMAHADPTELALSGLEAFSFDYIVKWPLSLIINR
KALTRYQMLFRHMFYCKHVERQLCSVWISNKTAKQHSLHSAQWFAGAFTLRQRMLNFVQN
IQYYMMFEVMEPTWHILEKNLKSASNIDDVLGHHTGFLDTCLKDCMLTNPELLKVFSKLM
SVCVMFTNCMQKFTQSMKLDGELGGQTLEHSTVLGLPAGAEERARKELARKHLAEHADTV
QLVSGFEATINKFDKNFSAHLLDLLARLSIYSTSDCEHGMASVISRLDFNGFYTERLERL
SAERSQKATPQVPVLRGPPAPAPRVAVTAQ
Sequence of entity 4 (l, m), FASTA
>9H9P_4 Tubulin gamma-1 chain (chains l, m)
MPREIITLQLGQCGNQIGFEFWKQLCAEHGISPEAIVEEFATEGTDRKDVFFYQADDEHY
IPRAVLLDLEPRVIHSILNSPYAKLYNPENIYLSEHGGGAGNNWASGFSQGEKIHEDIFD
IIDREADGSDSLEGFVLCHSIAGGTGSGLGSYLLERLNDRYPKKLVQTYSVFPNQDEMSD
VVVQPYNSLLTLKRLTQNADCLVVLDNTALNRIATDRLHIQNPSFSQINQLVSTIMSAST
TTLRYPGYMNNDLIGLIASLIPTPRLHFLMTGYTPLTTDQSVASVRKTTVLDVMRRLLQP
KNVMVSTGRDRQTNHCYIAILNIIQGEVDPTQVHKSLQRIRERKLANFIPWGPASIQVAL
SRKSPYLPSAHRVSGLMMANHTSISSLFERTCRQYDKLRKREAFLEQFRKEDMFKDNFDE
MDTSREIVQQLIDEYHAATRPDYISWGTQEQ
Sequence of entity 5 (C), FASTA
>9H9P_5 Mitotic-spindle organizing protein 2A (chains C)
MAAQGVGPGPGSAAPPGLEAARQKLALRRKKVLSTEEMELYELAQAAGGGIDPDVFKILV
DLLKLNVAPLAVFQMLKSMCAGQRLASEPQDPAAVSLPTSSVPETRGRDKGSAALGGVLA
LAERSNHEGSSQRMPRQPSATRLPKGGGPGKSPTQGST
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 2 |
Primary citation
Structural insights into the interplay between microtubule polymerases, gamma-tubulin complexes and their receptors. Zheng, A., Vermeulen, B.J.A., Wurtz, M. et al. Nat Commun (2025) 16:402-402. DOI 10.1038/s41467-024-55778-7 · PubMed
Other PDB entries of the same protein (UniProt Q96SN8 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8RX1 3.57 Å, CryoEM structure of the gTuRC-CM1dim complex
- 9SMX 3.67 Å, CM1-activated gTuRC in complex with nascent alpha-E254D mutant microtubules
- 9G40 4.3 Å, Structure of the Position 7 CMG-decorated gamma-Tubulin Ring Complex from Pig Brain
- 6X0V 4.5 Å, Structure of MZT2/GCP-NHD and CDK5Rap2 at position 13 of the gamma-TuRC
Browse structure collections
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