6QLD: Inner kinetochore CCAN-Cenp-A complex
Structure of inner kinetochore CCAN-Cenp-A complex. Determined by electron microscopy at 4.15 Å resolution. Released 2 Oct 2019.
- Method
- Electron microscopy
- Resolution
- 4.15 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Escherichia coli
- Chains
- 22
- Atoms
- 29,086
- Mol. weight
- 471.67 kDa
- Released
- 2 Oct 2019
Explore 6QLD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6QLD contains 132 α-helices and 74 β-strands across 19 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: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 139-145 | 7 | |
| α-helix | 156-169 | 14 | |
| β-strand | 178 | 1 | 18 |
| α-helix | 180-207 | 28 | |
| α-helix | 217-220 | 4 | |
| α-helix | 222-224 | 3 | |
Chain b: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-42 | 11 | |
| α-helix | 50-76 | 27 | |
| β-strand | 82 | 1 | 18 |
| α-helix | 83 | 1 | |
| α-helix | 84-94 | 11 | |
| β-strand | 97-99 | 3 | 19 |
Chain d: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-52 | 11 | |
| β-strand | 57-58 | 2 | 20 |
| α-helix | 60-87 | 28 | |
| β-strand | 92-93 | 2 | 21 |
| α-helix | 95-105 | 11 | |
| α-helix | 108-127 | 20 | |
Chain e: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 113-124 | 12 | |
| α-helix | 125-129 | 5 | |
| α-helix | 140-145 | 6 | |
| α-helix | 155-166 | 12 | |
| β-strand | 177-178 | 2 | 22 |
| α-helix | 180-207 | 28 | |
| β-strand | 212 | 1 | 23 |
| α-helix | 217-223 | 7 | |
Chain f: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-29 | 3 | |
| α-helix | 32-41 | 10 | |
| β-strand | 46 | 1 | 23 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 22 |
| α-helix | 84-93 | 10 | |
Chain g: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-39 | 11 | |
| α-helix | 48-74 | 27 | |
| α-helix | 82-89 | 8 | |
| α-helix | 93-98 | 6 | |
| β-strand | 102-104 | 3 | 19 |
Chain h: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-52 | 11 | |
| α-helix | 60-87 | 28 | |
| α-helix | 95-105 | 11 | |
| α-helix | 108-125 | 18 | |
Chain H: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-37 | 32 | |
| α-helix | 47-72 | 26 | |
| α-helix | 84-92 | 9 | |
| α-helix | 97-134 | 38 | |
11 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Inner kinetochore subunit MIF2 | C | protein | 22 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P35201 (AlphaFold model) |
| DNA (125-mer) | G | DNA | 124 | Escherichia coli | |
| Inner kinetochore subunit MCM16 | H | protein | 133 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q12262 (AlphaFold model) |
| Inner kinetochore subunit CTF3 | I | protein | 408 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q12748 (AlphaFold model) |
| DNA (125-mer) | J | DNA | 124 | Escherichia coli | |
| Inner kinetochore subunit MCM22 | K | protein | 122 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P47167 (AlphaFold model) |
| Inner kinetochore subunit IML3 | L | protein | 241 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P38265 |
| Inner kinetochore subunit CHL4 | N | protein | 447 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P38907 |
| Inner kinetochore subunit MCM21 | O | protein | 212 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q06675 |
| Inner kinetochore subunit CTF19 | P | protein | 270 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q02732 |
| Inner kinetochore subunit OKP1 | Q | protein | 231 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P53298 |
| Inner kinetochore subunit AME1 | U | protein | 190 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P38313 |
9 more molecules are not listed.
Sequence of entity 1 (C), FASTA
>6QLD_1 Inner kinetochore subunit MIF2 (chains C)
LRKSTRVKVAPLQYWRNEKIVY
Sequence of entity 2 (G), FASTA
>6QLD_2 DNA (125-MER) (chains G)
TCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCAC
Sequence of entity 3 (H), FASTA
>6QLD_3 Inner kinetochore subunit MCM16 (chains H)
SSEKQWERIQQLEKEHVEVYRELLITLDRLYLIRKHNHAVILSHTQQRLLEIRHQLQINL
EKTALLIRLLEKPDNTNVLFTKLQNLLEESNSLDYELLQSLGAQSSLHKQLIESRAERDE
LMSKLIELSSKFP
Sequence of entity 4 (I), FASTA
>6QLD_4 Inner kinetochore subunit CTF3 (chains I)
NSNVLLPRKVMSRDSLKHLYSSIILIKNSRDESSSPYEWCIWQLKRCFAHQIETPQEVIP
IIISVSSMDNKLSSRIIQTFCNLKYLKLDELTLKKVCGGILPLWKPELISGTREFFVKFM
ASIFMWSTRDGHDNNCTFSETCFYVLQMITNWVLDDKLIALGLTLLHDMQSLLTLDKIFN
NATSNRFSTMAFISSLDILTQLSKQTKSDYAIQYLIVGPDIMNKVFSSDDPLLLSAACRY
LVATKNKLMQYPSTNKFVRMQNQYIMDLTNYLYRNKVLSSKSLFGVSPDFFKQILENLYI
PTADFKNAKFFTITGIPALSYICIIILRRLETAENTKIKFTSGIINEETFNNFFRVHHDE
IGQHGWIKGVNNIHDLRVKILMHLSNTANPYRDIAAFLFTYLKSLSKY
Sequence of entity 5 (J), FASTA
>6QLD_5 DNA (125-MER) (chains J)
GTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACG
TGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTC
TCGA
Sequence of entity 6 (K), FASTA
>6QLD_6 Inner kinetochore subunit MCM22 (chains K)
VLDVYIKNLENQIGNKRYFLKQAQGAIDEITKRSLDTEGKPVNSEVFTELLRKPMFFSER
ADPIGFSLTSNFLSLRAQSSSEWLSLMNDQSVDQKAMLLLQNNINSDLKELLRKLQHQMT
IM
Sequence of entity 7 (L), FASTA
>6QLD_7 Inner kinetochore subunit IML3 (chains L)
PYTWKFLGISKQLSLENGIAKLNQLLNLEVDLDIQTIRVPSDPDGGTAADEYIRYEMRLD
ISNLDEGTYSKFIFLGNSKMEVPMFLCYCGTDNRNEVVLQWLKAEYGVIMWPIKFEQKTM
IKLADASIVHVTKENIEQITWFSSKLYFEPETQDKNLRQFSIEIPRESCEGLALGYGNTM
HPYNDAIVPYIYNETGMAVERLPLTSVILAGHTKIMRESIVTSTRSLRNRVLAVVLQSIQ
F
Sequence of entity 8 (N), FASTA
>6QLD_8 Inner kinetochore subunit CHL4 (chains N)
LRLEDNYVPTSDTLVVFKQLMKLPVTVLYDLTLSWFAKFGGSFDGDIYLLTETLDLLIEK
GVRRNVIVNRILYVYWPDGLNVFQLAEIDCHLMISKPEKFKWLPSKALRGDGKPYVVKLQ
PAKFIENLQTDLAKIYHCHVYMFKHPSLPVLITRIQLFDSNNLFLSTPNIGSINKESLYN
KLDKFQGKPLISRRPYYVAFPLNSPIIFHSVDKDIYARLVLQSISRTISERETIIFKPVQ
KIPVKSIHNIMTLLGPSRFAESMGPWECYASANFERSPLHDYKKHQGLTGKKVMVREFDD
SFLNDDENFYGKEEPEIRRLRLEKNMIKFKGSANGVMDQKYNDLKEFNEHVHNIRNGKKN
EDSGEPVYISRYSSLVPIEKVGFTLKNEINSRIITIKLKFNGNDIFGGLHELCDKNLINI
DKVPGWLAGENGSFSGTIMNGDFQREQ
Sequence of entity 9 (O), FASTA
>6QLD_9 Inner kinetochore subunit MCM21 (chains O)
STSDRSELEDYIVLENVYRMFGITFFPLVDPIDLKIKDASGEIFVDREMLGIRLEVFSER
TSQFEKPHYVLLKKRIKSNSWFLFKHTIPSFIDVQGIFDDTNGGLVISHDDAYLFAKRVF
LQLVEVQKRRQIFKDLEAKKIIHDLDLDLESSMVSFFVKDIKVELFVKQNEIVSCSILDD
IHDFSQNNKSKWEIALLGSLDDLELKLNHSFA
Sequence of entity 10 (P), FASTA
>6QLD_10 Inner kinetochore subunit CTF19 (chains P)
QNDITQDFLNLISISSSNPNSAISDRKRVERINGLTNLQKELVTKYDTLPLLNMNLRLSY
LRDHTYPHLQVSVQSRDRVHNDGIEVLVVNYKFCRNTMNPFEIQFKMFYKFEDSTLLKWE
ILRISTNVRLKAKQLLATRNFQKCLLSLYEFDKIKSKKTGIFQNLINLLKRKTRCYLMNN
SDSLIVERVIREGRLTTIKLQINFIITMPGERGKPRNCFLPMSKISIALWKGGERFNQID
LDEICYGLIKEYGVKTGLKEICNVCLFPDM
Sequence of entity 11 (Q), FASTA
>6QLD_11 Inner kinetochore subunit OKP1 (chains Q)
SILRLLETNTVSALDSVFEKYEKEMNQMTHGDNNEVKRIYSKKERLLEIILTKIKKKLRQ
AKFPSRISERDLDIEYIYSKRQFIQNRYSQELQNNERLEAILSREQNLLEETRKLCMNLK
TNNKKRLTEKLIQKDLHPVLNKAMEYTYGLESTNGFMHPDGPVTFRNDSHELNLMLNDPI
KSTADVRLDKEEVLSLLPSLKEYTKKSKELKETMGQMISDSHEEEIKEVFV
Sequence of entity 12 (U), FASTA
>6QLD_12 Inner kinetochore subunit AME1 (chains U)
SVTTIDVLSSLFINLFENDLIPQALKDFNKSDDDQFRKLLYKLDLRLFQTISDQMTRDLK
DILDINVSNNELCYQLKQVLARKEDLNQQIISVRNEIQELKAGKDWHDLQNEQAKLNDKV
KLNKRLNDLTSTLLGKYEGDRKIMSQDSEDDSIRDDSNILDIAHFVDLMDPYNGLLKKIN
KINENLSNEL
Primary citation
Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome. Yan, K., Yang, J., Zhang, Z. et al. Nature (2019) 574:278-282. DOI 10.1038/s41586-019-1609-1 · PubMed
Other PDB entries of the same protein (UniProt P35201 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2VPV 2.7 Å, Dimerization Domain of Mif2p
- 7ON1 3.35 Å, Cenp-A nucleosome in complex with Cenp-C
Browse structure collections
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