8UX1: Ran

Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle. Determined by electron microscopy at 2.5 Å resolution. Released 22 Nov 2023.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Drosophila melanogaster, synthetic construct, Homo sapiens
Chains: 12
Atoms: 16,395
Mol. weight: 272.23 kDa
Released: 22 Nov 2023

Explore 8UX1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UX1 contains 55 α-helices and 66 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.

Chain A: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-131	11

Chains B and F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-91	9
β-strand	96-98	3	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	4
α-helix	46-72	27
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	6
α-helix	113-115	3

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
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	102-120	19

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain G: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	13-16	4
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	3

Chain H: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
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	101-121	21

Chain K: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-17	9	11
α-helix	23-27	5
β-strand	40	1	12
β-strand	45	1	12
β-strand	48-49	2	11
β-strand	52	1	11
β-strand	59-65	7	11
α-helix	69-72	4
α-helix	78-81	4
β-strand	85-91	7	11
α-helix	95-98	4
α-helix	101-111	11
β-strand	117-122	6	11
α-helix	133-135	3
α-helix	136-140	5
β-strand	145-150	6	11
α-helix	159-169	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	A, E	protein	136	Drosophila melanogaster	P02299 (AlphaFold model)
Histone H4	B, F	protein	104	Drosophila melanogaster	P84040 (AlphaFold model)
Histone H2A	C, G	protein	124	Drosophila melanogaster	P84051 (AlphaFold model)
Histone H2B	D, H	protein	125	Drosophila melanogaster	P02283 (AlphaFold model)
153-bp Widom 601 DNA forward strand	I	DNA	153	synthetic construct
153-bp Widom 601 DNA reverse strand	J	DNA	153	synthetic construct
GTP-binding nuclear protein Ran	K	protein	216	Homo sapiens	P62826
Regulator of chromosome condensation	L	protein	420	Homo sapiens	P18754

Sequence of entity 1 (A, E), FASTA

>8UX1_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>8UX1_2 Histone H4 (chains B, F)
MITGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVL
KVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>8UX1_3 Histone H2A (chains C, G)
MSGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA
EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKT
EKKA

Sequence of entity 4 (D, H), FASTA

>8UX1_4 Histone H2B (chains D, H)
GMIPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMS
IMNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK

Sequence of entity 5 (I), FASTA

>8UX1_5 153-bp Widom 601 DNA forward strand (chains I)
ATCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGT
TAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAA
TTGAGCGGCCTCGGCACCGGGATTCTCCAGGAT

Sequence of entity 6 (J), FASTA

>8UX1_6 153-bp Widom 601 DNA reverse strand (chains J)
ATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCT
TAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCT
CCAGGCACGTGTCAGATATATACATCCTGTGAT

Sequence of entity 7 (K), FASTA

>8UX1_7 GTP-binding nuclear protein Ran (chains K)
MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIK
FNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLC
GNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMP
ALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Sequence of entity 8 (L), FASTA

>8UX1_8 Regulator of chromosome condensation (chains L)
SPKRIAKRRSPPADAIPKSKKVKVSHRSHSTEPGLVLTLGQGDVGQLGLGENVMERKKPA
LVSIPEDVVQAEAGGMHTVCLSKSGQVYSFGCNDEGALGRDTSVEGSEMVPGKVELQEKV
VQVSAGDSHTAALTDDGRVFLWGSFRDNNGVIGLLEPMKKSMVPVQVQLDVPVVKVASGN
DHLVMLTADGDLYTLGCGEQGQLGRVPELFANRGGRQGLERLLVPKCVMLKSRGSRGHVR
FQDAFCGAYFTFAISHEGHVYGFGLSNYHQLGTPGTESCFIPQNLTSFKNSTKSWVGFSG
GQHHTVCMDSEGKAYSLGRAEYGRLGLGEGAEEKSIPTLISRLPAVSSVACGASVGYAVT
KDGRVFAWGMGTNYQLGTGQDEDAWSPVEMMGKQLENRVVLSVSSGGQHTVLLVKDKEQS

Primary citation

Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle. Huang, S.K., Rubinstein, J.L., Kay, L.E. To be published.

Other PDB entries of the same protein (UniProt P02299 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6AT0 1.28 Å, Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone…
6MHA 1.5 Å, dHP1 Chromodomain Y24W variant bound to histone H3 peptide containing trimethyllysine
6ASZ 1.52 Å, Chromodomain HP1 with Y24F mutation bound to histone H3 peptide containing trimethyl…
7VRF 1.7 Å, Crystal structure of Oxpecker chromodomain in complex with H3K9me3
1KNA 2.1 Å, Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9.
9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
2NQB 2.3 Å, Drosophila Nucleosome Structure
9ZQC 2.37 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2
1KNE 2.4 Å, Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9
2PYO 2.43 Å, Drosophila nucleosome core
4QUF 2.5 Å, crystal structure of chromodomain of Rhino with H3K9me3
2YBA 2.55 Å, Crystal structure of Nurf55 in complex with histone H3

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