2VE7: Bonsai version of the human Ndc80 complex

Crystal structure of a bonsai version of the human Ndc80 complex. Determined by X-ray diffraction at 2.88 Å resolution. Released 13 May 2008.

Method: X-ray diffraction
Resolution: 2.88 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 8,258
Mol. weight: 131.06 kDa
Ligands: IPH
Released: 13 May 2008

Explore 2VE7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VE7 contains 48 α-helices and 17 β-strands across 4 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: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	89-105	17
α-helix	115-117	3
α-helix	122-133	12
α-helix	147-157	11
α-helix	166-170	5
α-helix	178-200	23
β-strand	214	1	1
β-strand	220	1	1
α-helix	222-238	17
α-helix	244-258	15
α-helix	264-1125	31
α-helix	1131-1141	11
α-helix	1216-1219	4

Chain B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	89-105	17
α-helix	122-134	13
α-helix	147-157	11
α-helix	166-170	5
α-helix	178-198	21
β-strand	214	1	2
β-strand	220	1	2
α-helix	222-236	15
α-helix	244-257	14
α-helix	272-1141	39
β-strand	1144-1147	4	3
β-strand	1154-1158	5	3
β-strand	1162	1	4
β-strand	1165	1	4
β-strand	1170-1175	6	3
β-strand	1182-1183	2	3
α-helix	1195-1203	9
α-helix	1207-1221	15

Chain C: 13 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	11-21	11
α-helix	25-29	5
α-helix	33-35	3
α-helix	42-57	16
α-helix	62-64	3
α-helix	76-79	4
α-helix	83-98	16
α-helix	106-110	5
α-helix	114-144	31
α-helix	147-164	18
α-helix	1137-1147	11
β-strand	1150-1151	2	5
β-strand	1160-1163	4	5
β-strand	1172-1175	4	5
α-helix	1182-1190	9

Chain D: 14 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	11-21	11
α-helix	26-30	5
α-helix	33-35	3
α-helix	42-57	16
α-helix	61-65	5
α-helix	66-68	3
α-helix	76-79	4
α-helix	83-98	16
α-helix	106-110	5
α-helix	114-148	35
α-helix	150-1122	21
α-helix	1127-1131	5
α-helix	1132-1147	16
β-strand	1149-1152	4	6
β-strand	1160-1165	6	6
β-strand	1170-1171	2	6
β-strand	1174-1175	2	6
α-helix	1182-1191	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinetochore protein HEC1, kinetochore protein SPC25	A, B	protein	315	HOMO SAPIENS	O14777 (AlphaFold model), Q9HBM1 (AlphaFold model)
Kinetochore protein NUF2, kinetochore protein SPC24	C, D	protein	250	HOMO SAPIENS	Q8NBT2 (AlphaFold model), Q9BZD4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2VE7_1 KINETOCHORE PROTEIN HEC1, KINETOCHORE PROTEIN SPC25 (chains A, B)
MIKDPRPLNDKAFIQQCIRQLCEFLTENGYAHNVSMKSLQAPSVKDFLKIFTFLYGFLCP
SYELPDTKFEEEVPRIFKDLGYPFALSKSSMYTVGAPHTWPHIVAALVWLIDCIKIHTAM
KESSPLFDDGQPWGEETEDGIMHNKLFLDYTIKCYESFMSGADSFDEMNAELQSKLKDLF
NVDAFKLESLEAKNRALNEQIARLEQERSTANKANAERLKRLQKSADLYKDRLGLEIRKI
YGEKLQFIFTNIDPKNPESPFMFSLHLNEARDYEVSDSAPHLEGLAEFQENVRKTNNFSA
FLANVRKAFTATVYQ

Sequence of entity 2 (C, D), FASTA

>2VE7_2 KINETOCHORE PROTEIN NUF2, KINETOCHORE PROTEIN SPC24 (chains C, D)
GPLGSMETLSFPRYNVAEIVIHIRNKILTGADGKNLTKNDLYPNPKPEVLHMIYMRALQI
VYGIRLEHFYMMPVNSGVMYPHLMEGFLPFSNLVTHLDSFLPICRVNDFETADILCPKAK
RTSRFLSGIINFIHFREACRETYMEFLWQYKSSADKMQQLNAAHQEALMKLERLEKEVDE
DTTVTIPSAVYVAQLYHQVSKIEWEYECEPGMVKGIHHGPSVAQPIHLDSTQLSRKFISD
YLWSLVDTEW

Ligands and cofactors

ID	Name	Formula	Copies
IPH	Phenol	C6 H6 O	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Implications for Kinetochore-Microtubule Attachment from the Structure of an Engineered Ndc80 Complex. Ciferri, C., Pasqualato, S., Screpanti, E. et al. Cell (2008) 133:427. DOI 10.1016/J.CELL.2008.03.020 · PubMed

Other PDB entries of the same protein (UniProt O14777 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2IGP 1.8 Å, Crystal Structure of Hec1 CH domain
8G0P 2.0 Å, Crystal structure of the human Ndc80:Nuf2 loop region
9N9G 3.0 Å, Cryo-EM structure of the human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized…
3IZ0 8.6 Å, Human Ndc80 Bonsai Decorated Microtubule

Browse structure collections

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