3MVD: Chromatin factor RCC1

Crystal structure of the chromatin factor RCC1 in complex with the nucleosome core particle. Determined by X-ray diffraction at 2.9 Å resolution. Released 25 Aug 2010.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Xenopus laevis, Drosophila melanogaster
Chains: 12
Atoms: 17,743
Mol. weight: 289.62 kDa
Released: 25 Aug 2010

Explore 3MVD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3MVD contains 50 α-helices and 86 β-strands across 10 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.

Chains A and E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-76	13
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	96-98	3	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-35	9
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	101-119	19

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-35	9
β-strand	42-43	2	9
α-helix	46-71	26
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	101-120	20

Chain K: 6 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	32-38	7
β-strand	42-49	8	11
β-strand	63-69	7	11
α-helix	70-71	2
β-strand	76-81	6	11
β-strand	85-90	6	11
β-strand	95-99	5	11
β-strand	120-121	2	11
β-strand	128-133	6	12
β-strand	137-142	6	12
β-strand	147-151	5	12
β-strand	153-154	2	13
β-strand	159-161	3	13
β-strand	163	1	14
β-strand	166	1	14
β-strand	168-173	6	12
β-strand	180-185	6	15
β-strand	189-194	6	15
β-strand	199-203	5	15
β-strand	233-235	3	15
α-helix	241-242	2
β-strand	243-249	7	16
β-strand	252-257	6	16
α-helix	262	1
β-strand	263-268	6	16
β-strand	283-290	8	16
β-strand	295-300	6	17
β-strand	304-309	6	17
β-strand	314-318	5	17
α-helix	321-323	3
β-strand	334-339	6	17
α-helix	346	1
β-strand	347-353	7	18
β-strand	356-361	6	18
β-strand	366-370	5	18
β-strand	385-390	6	18
β-strand	401-406	6	11
β-strand	410-416	7	11

1 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
Histone H3.2	A, E	protein	135	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	102	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	C, G	protein	129	Xenopus laevis	Q6AZJ8 (AlphaFold model)
Histone H2B 1.1	D, H	protein	122	Xenopus laevis	P02281 (AlphaFold model)
DNA (146-mer)	I	DNA	147
DNA (146-mer)	J	DNA	147
Regulator of chromosome condensation	K, L	protein	423	Drosophila melanogaster	P25171

Sequence of entity 1 (A, E), FASTA

>3MVD_1 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>3MVD_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>3MVD_3 Histone H2A (chains C, G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>3MVD_4 Histone H2B 1.1 (chains D, H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 5 (I), FASTA

>3MVD_5 DNA (146-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT

Sequence of entity 6 (J), FASTA

>3MVD_6 DNA (146-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT

Sequence of entity 7 (K, L), FASTA

>3MVD_7 Regulator of chromosome condensation (chains K, L)
GSPRRKALTNNNNAGEAEQQPPKAKRARIAFHLELPKRRTVLGNVLVCGNGDVGQLGLGE
DILERKRLSPVAGIPDAVDISAGGMHNLVLTKSGDIYSFGCNDEGALGRDTSEDGSESKP
DLIDLPGKALCISAGDSHSACLLEDGRVFAWGSFRDSHGNMGLTIDGNKRTPIDLMEGTV
CCSIASGADHLVILTTAGKVFTVGCAEQGQLGRLSERSISGEGRRGKRDLLRPTQLIITR
AKPFEAIWATNYCTFMRESQTQVIWATGLNNFKQLAHETKGKEFALTPIKTELKDIRHIA
GGQHHTVILTTDLKCSVVGRPEYGRLGLGDVKDVVEKPTIVKKLTEKIVSVGCGEVCSYA
VTIDGKLYSWGSGVNNQLGVGDGDDELEPIVVVSKNTQGKHMLLASGGGQHAIFLVKADK
QDQ

Primary citation

Structure of RCC1 chromatin factor bound to the nucleosome core particle. Makde, R.D., England, J.R., Yennawar, H.P. et al. Nature (2010) 467:562-566. DOI 10.1038/nature09321 · PubMed

Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome

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