8PPR: Human outer kinetochore KMN network complex
Structure of the human outer kinetochore KMN network complex. Determined by electron microscopy at 3.0 Å resolution. Released 20 Mar 2024.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 11,354
- Mol. weight
- 465.59 kDa
- Released
- 20 Mar 2024
Explore 8PPR in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8PPR contains 60 α-helices and 25 β-strands across 8 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 D: 12 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 98-102 | 5 | |
| α-helix | 110-112 | 3 | |
| α-helix | 119-123 | 5 | |
| α-helix | 130-152 | 23 | |
| α-helix | 161-185 | 25 | |
| α-helix | 188-192 | 5 | |
| α-helix | 198-245 | 48 | |
| β-strand | 252 | 1 | 1 |
| α-helix | 256-259 | 4 | |
| α-helix | 265-269 | 5 | |
| α-helix | 271-273 | 3 | |
| α-helix | 275-325 | 51 | |
| α-helix | 332-337 | 6 | |
Chain F: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 87-147 | 61 | |
| β-strand | 149-151 | 3 | 5 |
| α-helix | 156 | 1 | |
| β-strand | 161-164 | 4 | 5 |
| β-strand | 171-174 | 4 | 5 |
| α-helix | 182-191 | 10 | |
Chain G: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 81-142 | 62 | |
| β-strand | 145-149 | 5 | 6 |
| β-strand | 153-158 | 6 | 6 |
| β-strand | 170-176 | 7 | 6 |
| β-strand | 182-184 | 3 | 6 |
| α-helix | 195-204 | 10 | |
| α-helix | 207-222 | 16 | |
Chain K: 14 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2098-2129 | 32 | |
| β-strand | 2136-2141 | 6 | 3 |
| β-strand | 2144-2149 | 6 | 3 |
| α-helix | 2150-2152 | 3 | |
| β-strand | 2154-2160 | 7 | 3 |
| α-helix | 2161-2164 | 4 | |
| α-helix | 2172-2174 | 3 | |
| α-helix | 2175 | 1 | |
| β-strand | 2176 | 1 | 7 |
| β-strand | 2177-2184 | 8 | 3 |
| β-strand | 2186 | 1 | 4 |
| α-helix | 2193-2208 | 16 | |
| α-helix | 2212-2215 | 4 | |
| β-strand | 2218 | 1 | 7 |
| α-helix | 2221-2249 | 29 | |
| α-helix | 2251-2253 | 3 | |
| β-strand | 2255-2260 | 6 | 8 |
| β-strand | 2264-2271 | 8 | 8 |
| β-strand | 2276-2283 | 8 | 8 |
| α-helix | 2292-2293 | 2 | |
| β-strand | 2296-2301 | 6 | 8 |
| α-helix | 2306-2315 | 10 | |
| α-helix | 2322-2331 | 10 | |
| α-helix | 2332-2336 | 5 | |
| α-helix | 2339-2341 | 3 | |
Chain M: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-13 | 7 | |
| α-helix | 17-49 | 33 | |
| α-helix | 57-85 | 29 | |
| α-helix | 86-90 | 5 | |
| α-helix | 92-94 | 3 | |
| α-helix | 100-105 | 6 | |
| α-helix | 111-168 | 58 | |
| α-helix | 174-204 | 31 | |
Chain N: 11 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 38-40 | 3 | 2 |
| α-helix | 43-58 | 16 | |
| α-helix | 59-62 | 4 | |
| α-helix | 66-68 | 3 | |
| α-helix | 70-85 | 16 | |
| β-strand | 88-90 | 3 | 2 |
| β-strand | 93-94 | 2 | 2 |
| α-helix | 105-150 | 46 | |
| β-strand | 153 | 1 | 1 |
| α-helix | 156-161 | 6 | |
| α-helix | 167-212 | 46 | |
| α-helix | 215-220 | 6 | |
| β-strand | 253-254 | 2 | 3 |
| α-helix | 265-268 | 4 | |
| α-helix | 271 | 1 | |
| β-strand | 272 | 1 | 4 |
| α-helix | 273 | 1 | |
Chain P: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-52 | 19 | |
| α-helix | 55-61 | 7 | |
| α-helix | 63-66 | 4 | |
| α-helix | 70-99 | 30 | |
| α-helix | 101-114 | 14 | |
| α-helix | 121-123 | 3 | |
| α-helix | 129-188 | 60 | |
| α-helix | 190-200 | 11 | |
Chain Z: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 184-220 | 37 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Kinetochore-associated protein DSN1 homolog | D | protein | 356 | Homo sapiens | Q9H410 (AlphaFold model) |
| Protein MIS12 homolog | M | protein | 205 | Homo sapiens | Q9H081 (AlphaFold model) |
| Kinetochore-associated protein NSL1 homolog | N | protein | 281 | Homo sapiens | Q96IY1 (AlphaFold model) |
| Polyamine-modulated factor 1 | P | protein | 205 | Homo sapiens | Q6P1K2 (AlphaFold model) |
| Kinetochore protein Spc24 | F | protein | 197 | Homo sapiens | Q8NBT2 |
| Kinetochore protein Spc25 | G | protein | 224 | Homo sapiens | Q9HBM1 |
| Kinetochore scaffold 1 | K | protein | 2342 | Homo sapiens | Q8NG31 |
| ZW10 interactor | Z | protein | 277 | Homo sapiens | O95229 |
Sequence of entity 1 (D), FASTA
>8PPR_1 Kinetochore-associated protein DSN1 homolog (chains D)
MTSVTRSEIIDEKGPVMSKTHDHQLESSLSPVEVFAKTSASLEMNQGVSEERIHLGSSPK
KGGNCDLSHQERLQSKSLHLSPQEQSASYQDRRQSWRRASMKETNRRKSLHPIHQGITEL
SRSISVDLAESKRLGCLLLSSFQFSIQKLEPFLRDTKGFSLESFRAKASSLSEELKHFAD
GLETDGTLQKCFEDSNGKASDFSLEASVAEMKEYITKFSLERQTWDQLLLHYQQEAKEIL
SRGSTEAKITEVKVEPMTYLGSSQNEVLNTKPDYQKILQNQSKVFDCMELVMDELQGSVK
QLQAFMDESTQCFQKVSVQLGKRSMQQLDPSPARKLLKLQLQNPPAIHGSGSGSCQ
Sequence of entity 2 (M), FASTA
>8PPR_2 Protein MIS12 homolog (chains M)
MSVDPMTYEAQFFGFTPQTCMLRIYIAFQDYLFEVMQAVEQVILKKLDGIPDCDISPVQI
RKCTEKFLCFMKGHFDNLFSKMEQLFLQLILRIPSNILLPEDKCKETPYSEEDFQHLQKE
IEQLQEKYKTELCTKQALLAELEEQKIVQAKLKQTLTFFDELHNVGRDHGTSDFRESLVS
LVQNSRKLQNIRDNVEKESKRLKIS
Sequence of entity 3 (N), FASTA
>8PPR_3 Kinetochore-associated protein NSL1 homolog (chains N)
MAGSPELVVLDPPWDKELAAGTESQALVSATPREDFRVRCTSKRAVTEMLQLCGRFVQKL
GDALPEEIREPALRDAQWTFESAVQENISINGQAWQEASDNCFMDSDIKVLEDQFDEIIV
DIATKRKQYPRKILECVIKTIKAKQEILKQYHPVVHPLDLKYDPDPAPHMENLKCRGETV
AKEISEAMKSLPALIEQGEGFSQVLRMQPVIHLQRIHQEVFSSCHRKPDAKPENFITQIE
TTPTETASRKTSDMVLKRKQTKDCPQRKWYPLRPKKINLDT
Sequence of entity 4 (P), FASTA
>8PPR_4 Polyamine-modulated factor 1 (chains P)
MAEASSANLGSGCEEKRHEGSSSESVPPGTTISRVKLLDTMVDTFLQKLVAAGSYQRFTD
CYKCFYQLQPAMTQQIYDKFIAQLQTSIREEISDIKEEGNLEAVLNALDKIVEEGKVRKE
PAWRPSGIPEKDLHSVMAPYFLQQRDTLRRHVQKQEAENQQLADAVLAGRRQVEELQLQV
QAQQQAWQALHREQRELVAVLREPE
Sequence of entity 5 (F), FASTA
>8PPR_5 Kinetochore protein Spc24 (chains F)
MAAFRDIEEVSQGLLSLLGANRAEAQQRRLLGRHEQVVERLLETQDGAEKQLREILTMEK
EVAQSLLNAKEQVHQGGVELQQLEAGLQEAGEEDTRLKASLLQLTRELEELKEIEADLER
QEKEVDEDTTVTIPSAVYVAQLYHQVSKIEWDYECEPGMVKGIHHGPSVAQPIHLDSTQL
SRKFISDYLWSLVDTEW
Sequence of entity 6 (G), FASTA
>8PPR_6 Kinetochore protein Spc25 (chains G)
MVEDELALFDKSINEFWNKFKSTDTSCQMAGLRDTYKDSIKAFAEKLSVKLKEEERMVEM
FLEYQNQISRQNKLIQEKKDNLLKLIAEVKGKKQELEVLTANIQDLKEEYSRKKETISTA
NKANAERLKRLQKSADLYKDRLGLEIRKIYGEKLQFIFTNIDPKNPESPFMFSLHLNEAR
DYEVSDSAPHLEGLAEFQENVRKTNNFSAFLANVRKAFTATVYN
Sequence of entity 7 (K), FASTA
>8PPR_7 Kinetochore scaffold 1 (chains K)
MDGVSSEANEENDNIERPVRRRHSSILKPPRSPLQDLRGGNERVQESNALRNKKNSRRVS
FADTIKVFQTESHMKIVRKSEMEGCSAMVPSQLQLLPPGFKRFSCLSLPETETGENLLLI
QNKKLEDNYCEITGMNTLLSAPIHTQMQQKEFSIIEHTRERKHANDQTVIFSDENQMDLT
SSHTVMITKGLLDNPISEKSTKIDTTSFLANLKLHTEDSRMKKEVNFSVDQNTSSENKID
FNDFIKRLKTGKCSAFPDVPDKENFEIPIYSKEPNSASSTHQMHVSLKEDENNSNITRLF
REKDDGMNFTQCHTANIQTLIPTSSETNSRESKGNDITIYGNDFMDLTFNHTLQILPATG
NFSEIENQTQNAMDVTTGYGTKASGNKTVFKSKQNTAFQDLSINSADKIHITRSHIMGAE
THIVSQTCNQDARILAMTPESIYSNPSIQGCKTVFYSSCNDAMEMTKCLSNMREEKNLLK
HDSNYAKMYCNPDAMSSLTEKTIYSGEENMDITKSHTVAIDNQIFKQDQSNVQIAAAPTP
EKEMMLQNLMTTSEDGKMNVNCNSVPHVSKERIQQSLSNPLSISLTDRKTELLSGENMDL
TESHTSNLGSQVPLAAYNLAPESTSESHSQSKSSSDECEEITKSRNEPFQRSDIIAKNSL
TDTWNKDKDWVLKILPYLDKDSPQSADCNQEIATSHNIVYCGGVLDKQITNRNTVSWEQS
LFSTTKPLFSSGQFSMKNHDTAISSHTVKSVLGQNSKLAEPLRKSLSNPTPDYCHDKMII
CSEEEQNMDLTKSHTVVIGFGPSELQELGKTNLEHTTGQLTTMNRQIAVKVEKCGKSPIE
KSGVLKSNCIMDVLEDESVQKPKFPKEKQNVKIWGRKSVGGPKIDKTIVFSEDDKNDMDI
TKSYTIEINHRPLLEKRDCHLVPLAGTSETILYTCRQDDMEITRSHTTALECKTVSPDEI
TTRPMDKTVVFVDNHVELEMTESHTVFIDYQEKERTDRPNFELSQRKSLGTPTVICTPTE
ESVFFPGNGESDRLVANDSQLTPLEEWSNNRGPVEVADNMELSKSATCKNIKDVQSPGFL
NEPLSSKSQRRKSLKLKNDKTIVFSENHKNDMDITQSCMVEIDNESALEDKEDFHLAGAS
KTILYSCGQDDMEITRSHTTALECKTLLPNEIAIRPMDKTVLFTDNYSDLEVTDSHTVFI
DCQATEKILEENPKFGIGKGKNLGVSFPKDNSCVQEIAEKQALAVGNKIVLHTEQKQQLF
AATNRTTNEIIKFHSAAMDEKVIGKVVDQACTLEKAQVESCQLNNRDRRNVDFTSSHATA
VCGSSDNYSCLPNVISCTDNLEGSAMLLCDKDEEKANYCPVQNDLAYANDFASEYYLESE
GQPLSAPCPLLEKEEVIQTSTKGQLDCVITLHKDQDLIKDPRNLLANQTLVYSQDLGEMT
KLNSKRVSFKLPKDQMKVYVDDIYVIPQPHFSTDQPPLPKKGQSSINKEEVILSKAGNKS
LNIIENSSAPICENKPKILNSEEWFAAACKKELKENIQTTNYNTALDFHSNSDVTKQVIQ
THVNAGEAPDPVITSNVPCFHSIKPNLNNLNGKTGEFLAFQTVHLPPLPEQLLELGNKAH
NDMHIVQATEIHNINIISSNAKDSRDEENKKSHNGAETTSLPPKTVFKDKVRRCSLGIFL
PRLPNKRNCSVTGIDDLEQIPADTTDINHLETQPVSSKDSGIGSVAGKLNLSPSQYINEE
NLPVYPDEINSSDSINIETEEKALIETYQKEISPYENKMGKTCNSQKRTWVQEEEDIHKE
KKIRKNEIKFSDTTQDREIFDHHTEEDIDKSANSVLIKNLSRTPSSCSSSLDSIKADGTS
LDFSTYRSSQMESQFLRDTICEESLREKLQDGRITIREFFILLQVHILIQKPRQSNLPGN
FTVNTPPTPEDLMLSQYVYRPKIQIYREDCEARRQKIEELKLSASNQDKLLVDINKNLWE
KMRHCSDKELKAFGIYLNKIKSCFTKMTKVFTHQGKVALYGKLVQSAQNEREKLQIKIDE
MDKILKKIDNCLTEMETETKNLEDEEKNNPVEEWDSEMRAAEKELEQLKTEEEELQRNLL
ELEVQKEQTLAQIDFMQKQRNRTEELLDQLSLSEWDVVEWSDDQAVFTFVYDTIQLTITF
EESVVGFPFLDKRYRKIVDVNFQSLLDEDQAPPSSLLVHKLIFQYVEEKESWKKTCTTQH
QLPKMLEEFSLVVHHCRLLGEEIEYLKRWGPNYNLMNIDINNNELRLLFSSSAAFAKFEI
TLFLSAYYPSVPLPSTIQNHVGNTSQDDIATILSKVPLENNYLKNVVKQIYQDLFQDCHF
YH
Sequence of entity 8 (Z), FASTA
>8PPR_8 ZW10 interactor (chains Z)
MEAAETEAEAAALEVLAEVAGILEPVGLQEEAELPAKILVEFVVDSQKKDKLLCSQLQVA
DFLQNILAQEDTAKGLDPLASEDTSRQKAIAAKEQWKELKATYREHVEAIKIGLTKALTQ
MEEAQRKRTQLREAFEQLQAKKQMAMEKRRAVQNQWQLQQEKHLQHLAEVSAEVRERKTG
TQQELDRVFQKLGNLKQQAEQERDKLQRYQTFLQLLYTLQGKLLFPEAEAEAENLPDDKP
QQPTRPQEQSTGDTMGRDPGVSFKAVGLQPAGDVNLP
Primary citation
Structure of the human outer kinetochore KMN network complex. Yatskevich, S., Yang, J., Bellini, D. et al. Nat Struct Mol Biol (2024) 31:874-883. DOI 10.1038/s41594-024-01249-y · PubMed
Other PDB entries of the same protein (UniProt Q9H410 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5LSI 2.0 Å, Crystal structure of the kinetochore MIS12 complex HEAD2 subdomain containing DSN1 and…
- 5LSJ 3.25 Å, Crystal structure of the human kinetochore MIS12-cenp-C delta-HEAD2 complex
- 5LSK 3.5 Å, Crystal structure of the human kinetochore MIS12-cenp-C complex
- 8Q5H 4.5 Å, Human KMN network (outer kinetochore)
Browse structure collections
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