ISDA

Entry Detail

PDB ID:

8XRJ

EMDB ID:

EMD-38604

Keywords:

TRANSCRIPTION/DNA/RNA

Title:

RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei

Biological Source:

Source Organism:

Homo sapiens

Host Organism:

Homo sapiens

PDB Version:

Deposition Date:

2024-01-07

Release Date:

2025-05-07

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.60 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB1
Chain IDs:A
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P24928 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB2
Chain IDs:B
Chain Length:1174
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P30876 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB3
Chain IDs:C
Chain Length:292
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P19387 Pfam ID:PF01193, PF01000

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB4
Chain IDs:D
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:O15514 Pfam ID:PF03874

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC1
Chain IDs:E
Chain Length:210
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P19388 Pfam ID:PF03871, PF01191

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Chain IDs:F
Chain Length:127
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P61218 Pfam ID:PF01192

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB7
Chain IDs:G
Chain Length:172
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62487 Pfam ID:PF03876, PF00575

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Chain IDs:H
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P52434 Pfam ID:PF03870

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB9
Chain IDs:I
Chain Length:125
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P36954 Pfam ID:PF02150, PF01096

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Chain IDs:J
Chain Length:67
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P62875 Pfam ID:PF01194

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerase II subunit RPB11-a
Chain IDs:K
Chain Length:117
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P52435 Pfam ID:PF13656

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA-directed RNA polymerases I, II, and III subunit RPABC4
Chain IDs:L
Chain Length:58
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P53803 Pfam ID:PF03604

Polymer Type:polydeoxyribonucleotide
Description:DNA
Chain IDs:M (auth: N)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polyribonucleotide
Description:RNA
Chain IDs:N (auth: P)
Chain Length:11
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Description:DNA
Chain IDs:O (auth: T)
Chain Length:158
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Description:Histone H3.1
Chain IDs:P (auth: a), T (auth: e)
Chain Length:135
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P68431 Pfam ID:PF00125

Protein Blast

Polymer Type:polypeptide(L)
Description:Histone H4
Chain IDs:Q (auth: b), U (auth: f)
Chain Length:1174
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P62805 Pfam ID:PF15511

Protein Blast

Polymer Type:polypeptide(L)
Description:Histone H2A type 1-B/E
Chain IDs:R (auth: c), V (auth: g)
Chain Length:292
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P04908 Pfam ID:PF00125, PF16211

Protein Blast

Polymer Type:polypeptide(L)
Description:Histone H2B type 1-J
Chain IDs:S (auth: d), W (auth: h)
Chain Length:142
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:P06899 Pfam ID:PF00125

Ligand Molecules

Primary Citation

Multiple structures of RNA polymerase II isolated from human nuclei by ChIP-CryoEM analysis

Kujirai, T, Kato, J, Yamamoto, K, Hirai, S, Fujii, T, Maehara, K, Harada, A, Negishi, L, Ogasawara, M, Yamaguchi, Y, Ohkawa, Y, Takizawa, Y, Kurumizaka, H.Show

To Be Published ? ? ? (?)

Primary Citation of related structures