4ACO: Budding yeast Ndc10 N-terminal domain

Structure of the budding yeast Ndc10 N-terminal domain. Determined by X-ray diffraction at 1.89 Å resolution. Released 11 Jan 2012.

Method: X-ray diffraction
Resolution: 1.89 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 1
Atoms: 3,879
Mol. weight: 112.07 kDa
Released: 11 Jan 2012

Explore 4ACO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ACO contains 33 α-helices and 10 β-strands across 1 chain. 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: 33 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	45-58	14
α-helix	82-89	8
α-helix	90-94	5
α-helix	108-138	31
α-helix	148-167	20
α-helix	184-193	10
α-helix	208-224	17
α-helix	228-231	4
β-strand	235	1	1
α-helix	236-238	3
β-strand	239-241	3	2
β-strand	249-255	7	2
β-strand	266-272	7	2
α-helix	278-280	3
α-helix	282-295	14
β-strand	297	1	3
β-strand	301	1	3
α-helix	309-311	3
α-helix	318-320	3
β-strand	322	1	1
α-helix	332-334	3
α-helix	335-348	14
α-helix	356-359	4
α-helix	361-362	2
β-strand	368-370	3	2
α-helix	371-377	7
α-helix	380-383	4
α-helix	390-392	3
α-helix	396-398	3
α-helix	401-407	7
α-helix	426-428	3
α-helix	429-432	4
α-helix	438-444	7
α-helix	447-449	3
α-helix	452-478	27
α-helix	483-486	4
α-helix	488-491	4
α-helix	493-503	11
α-helix	504-506	3
β-strand	511	1	4
α-helix	521-524	4
β-strand	526	1	4
α-helix	527-531	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Centromere DNA-binding protein complex CBF3 subunit A	A	protein	956	SACCHAROMYCES CEREVISIAE	P32504 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4ACO_1 CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT A (chains A)
MRSSILFLLKLMKIMDVQQQQEAMSSEDRFQELVDSLKPRTAHQYKTYYTKYIQWCQLNQ
IIPTPEDNSVNSVPYKDLPISAELIHWFLLDTLITDDKPGEKREETEDLDEEEENSFKIA
TLKKIIGSLNFLSKLCKVHENPNANIDTKYLESVTKLHTHWIDSQKAITTNETNNTNTQV
LCPPLLKVSLNLWNPETNHLSEKFFKTCSEKLRFLVDFQLRSYLNLSFEERSKIRFGSLK
LGKRDRDAIIYHKVTHSAEKKDTPGHHQLLALLPQDCPFICPQTTLAAYLYLRFYGIPSV
SKGDGFPNLNADENGSLLQDIPILRGKSLTTYPREETFSNYYTTVFRYCHLPYKRREYFN
KCNLVYPTWDEDTFRTFFNEENHGNWLEQPEAFAFPDKIPFDFKKIMNFKSPYTSYSTNA
KKDPFPPPKDLLVQIFPEIDEYKRHDYEGLSQNSRDFLDLMEVLRERFLSNLPWIYKFFP
NHDIFQDPIFGNSDFQSYFNDKTIHSKGSPILSFDILPGFNKIYKNKTNFYSLLIERPSQ
LTFASSHNPDTHPTQKQESEGPLQMSQLDTTQLNELLKQQSFEYVQFQTLSNFQILLSVF
NKIFEKLEMKKSSRGYILHQLNLFKITLDERIKKSKIDDADKFIRDNQPIKKEENIVNED
GPNTSRRTKRPKQIRLLSIADSSDESSTEDSNVFKKDGESIEDGAYGENEDENDSEMQEQ
LKSMINELINSKISTFLRDQMDQFELKINALLDKILEEKVTRIIEQKLGSHTGKFSTLKR
PQLYMTEEHNVGFDMEVPKKLRTSGKYAETVKDNDDHQAMSTTASPSPEQDQEAKSYTDE
QEFMLDKSIDSIEGIILEWFTPNAKYANQCVHSMNKSGNKSWRANCEALYKERKSIVEFY
IYLVNHESLDRYKAVDICEKLRDQNEGSFSRLAKFLRKWRHDHQNSFDGLLVYLSN

Primary citation

The Structure of the Yeast Kinetochore Ndc10 DNA-Binding Domain Reveals an Unexpected Evolutionary Relationship to Tyrosine Recombinases. Perriches, T., Singleton, M.R. J Biol Chem (2012) 287:5173. DOI 10.1074/JBC.C111.318501 · PubMed

Other PDB entries of the same protein (UniProt P32504 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6GYU 3.0 Å, Cryo-EM structure of the CBF3-msk complex of the budding yeast kinetochore
10EH 3.5 Å, De novo assembled CBF3-CEN complex
6GYP 3.6 Å, Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore
6GSA 4.2 Å, Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10
6GYS 4.4 Å, Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore

Browse structure collections

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