RNA 3D Hub //

Equivalence class NR_3.5_34359.12 Obsolete

Showing 1 to 14 of 14 entries
#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
12NVQ|1|R (rep)5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3'synthetic constructRNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTPX-ray diffraction2.9102006-12-12
26UPZ|1|RRNAsynthetic constructRNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 3X-ray diffraction3.1102020-06-10
32E2I|1|R5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3'RNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dGTPX-ray diffraction3.41102006-12-19
47KEE|1|RRNAsynthetic constructRNA polymerase II elongation complex with unnatural base dTPT3, rNaMTP bound to E-siteX-ray diffraction3.45102021-06-23
51R9T|1|RRNA strandRNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDEX-ray diffraction3.5102004-11-16
62YU9|1|R5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3'synthetic constructRNA polymerase II elongation complex in 150 mm MG+2 with UTPX-ray diffraction3.4102007-04-24
79BVT|1|XRNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3')synthetic constructRNA Pol II - High Mn(+2) concentrationX-ray diffraction3.4102024-10-02
88B3D|1|PRNAHomo sapiensStructure of the Pol II-TCR-ELOF1 complex.Electron microscopy2.6102023-09-27
97OOB|1|PRNAHomo sapiensPol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)Electron microscopy2.7102021-10-13
107OO3|1|PRNAHomo sapiensPol II-CSB-CSA-DDB1-UVSSA (Structure1)Electron microscopy2.8102021-10-06
118B3F|1|PRNAHomo sapiensPol II-CSB-CSA-DDB1-ELOF1Electron microscopy3.1102023-09-27
128TVY|1|RRNAsynthetic constructCryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state)Electron microscopy3.1102024-01-24
138TUG|1|RRNAsynthetic constructCryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state)Electron microscopy3.5102024-01-24
147Z2Z|1|RRNASaccharomyces cerevisiae S288CStructure of yeast RNA Polymerase III-DNA-Ty1 integrase complex (Pol III-DNA-IN1) at 3.1 AElectron microscopy3.0732023-04-05

Release history

Release3.3553.3563.3573.3583.3593.3603.3613.3623.3633.3643.3653.3663.3673.3683.3693.3703.3713.3723.3733.3743.3753.3763.377
Date2024-10-022024-10-092024-10-162024-10-232024-10-302024-11-062024-11-132024-11-202024-11-272024-12-042024-12-112024-12-182024-12-252025-01-012025-01-082025-01-152025-01-222025-01-292025-02-052025-02-122025-02-192025-02-262025-03-05

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

Instances are ordered to put similar structures near each other. Select one instance to see its 3D structure. Selecting two or more instances will show their superposition, but only chains with identical numbers of observed nucleotides will superpose well. Large structures are slow to display; this tool is not designed for that.

Showing 1 to 14 of 14 entries
#SViewPDBTitleMethodResolution#NTs
19BVT|1|XRNA Pol II - High Mn(+2) concentrationX-RAY DIFFRACTION3.410
27Z2Z|1|RStructure of yeast RNA Polymerase III-DNA-Ty1 integrase complex (Pol III-DNA-IN1) at 3.1 AELECTRON MICROSCOPY3.073
32NVQ|1|RRNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTPX-RAY DIFFRACTION2.910
47OO3|1|PPol II-CSB-CSA-DDB1-UVSSA (Structure1)ELECTRON MICROSCOPY2.810
57OOB|1|PPol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)ELECTRON MICROSCOPY2.710
68B3F|1|PPol II-CSB-CSA-DDB1-ELOF1ELECTRON MICROSCOPY3.110
78B3D|1|PStructure of the Pol II-TCR-ELOF1 complex.ELECTRON MICROSCOPY2.610
88TVY|1|RCryo-EM structure of CPD lesion containing RNA Polymerase II elongation complex with Rad26 and Elf1 (closed state)ELECTRON MICROSCOPY3.110
98TUG|1|RCryo-EM structure of CPD-stalled Pol II in complex with Rad26 (engaged state)ELECTRON MICROSCOPY3.510
106UPZ|1|RRNA polymerase II elongation complex with 5-guanidinohydantoin lesion in state 3X-RAY DIFFRACTION3.110
117KEE|1|RRNA polymerase II elongation complex with unnatural base dTPT3, rNaMTP bound to E-siteX-RAY DIFFRACTION3.4510
122E2I|1|RRNA polymerase II elongation complex in 5 mM Mg+2 with 2'-dGTPX-RAY DIFFRACTION3.4110
132YU9|1|RRNA polymerase II elongation complex in 150 mm MG+2 with UTPX-RAY DIFFRACTION3.410
141R9T|1|RRNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDEX-RAY DIFFRACTION3.510

Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. The ordering in the heat map is the same as in the table. The colorbar ranges from 0 to the maximum observed discrepancy. Click above the diagonal to select a range of structures, below the diagonal to select two structures.

9BVT|1|X:9BVT|1|X = 09BVT|1|X:7Z2Z|1|R = 0.22799BVT|1|X:2NVQ|1|R = 0.37299BVT|1|X:7OO3|1|P = 0.37669BVT|1|X:7OOB|1|P = 0.39649BVT|1|X:8B3F|1|P = 0.37839BVT|1|X:8B3D|1|P = 0.37839BVT|1|X:8TVY|1|R = 0.35949BVT|1|X:8TUG|1|R = 0.38269BVT|1|X:6UPZ|1|R = 0.47829BVT|1|X:7KEE|1|R = 0.38889BVT|1|X:2E2I|1|R = 0.39419BVT|1|X:2YU9|1|R = 0.40609BVT|1|X:1R9T|1|R = 0.39127Z2Z|1|R:9BVT|1|X = 0.22797Z2Z|1|R:7Z2Z|1|R = 07Z2Z|1|R:2NVQ|1|R = 0.29137Z2Z|1|R:7OO3|1|P = 0.36547Z2Z|1|R:7OOB|1|P = 0.35637Z2Z|1|R:8B3F|1|P = 0.35707Z2Z|1|R:8B3D|1|P = 0.35707Z2Z|1|R:8TVY|1|R = 0.56547Z2Z|1|R:8TUG|1|R = 0.60967Z2Z|1|R:6UPZ|1|R = 0.72927Z2Z|1|R:7KEE|1|R = 0.44337Z2Z|1|R:2E2I|1|R = 0.35437Z2Z|1|R:2YU9|1|R = 0.41267Z2Z|1|R:1R9T|1|R = 0.45302NVQ|1|R:9BVT|1|X = 0.37292NVQ|1|R:7Z2Z|1|R = 0.29132NVQ|1|R:2NVQ|1|R = 02NVQ|1|R:7OO3|1|P = 0.13882NVQ|1|R:7OOB|1|P = 0.17262NVQ|1|R:8B3F|1|P = 0.15112NVQ|1|R:8B3D|1|P = 0.15112NVQ|1|R:8TVY|1|R = 0.21542NVQ|1|R:8TUG|1|R = 0.21862NVQ|1|R:6UPZ|1|R = 0.27222NVQ|1|R:7KEE|1|R = 0.18812NVQ|1|R:2E2I|1|R = 0.19982NVQ|1|R:2YU9|1|R = 0.20342NVQ|1|R:1R9T|1|R = 0.31167OO3|1|P:9BVT|1|X = 0.37667OO3|1|P:7Z2Z|1|R = 0.36547OO3|1|P:2NVQ|1|R = 0.13887OO3|1|P:7OO3|1|P = 07OO3|1|P:7OOB|1|P = 0.05557OO3|1|P:8B3F|1|P = 0.05707OO3|1|P:8B3D|1|P = 0.05707OO3|1|P:8TVY|1|R = 0.14227OO3|1|P:8TUG|1|R = 0.15107OO3|1|P:6UPZ|1|R = 0.27087OO3|1|P:7KEE|1|R = 0.21017OO3|1|P:2E2I|1|R = 0.27717OO3|1|P:2YU9|1|R = 0.26757OO3|1|P:1R9T|1|R = 0.33667OOB|1|P:9BVT|1|X = 0.39647OOB|1|P:7Z2Z|1|R = 0.35637OOB|1|P:2NVQ|1|R = 0.17267OOB|1|P:7OO3|1|P = 0.05557OOB|1|P:7OOB|1|P = 07OOB|1|P:8B3F|1|P = 0.06357OOB|1|P:8B3D|1|P = 0.06357OOB|1|P:8TVY|1|R = 0.13677OOB|1|P:8TUG|1|R = 0.14797OOB|1|P:6UPZ|1|R = 0.29687OOB|1|P:7KEE|1|R = 0.24317OOB|1|P:2E2I|1|R = 0.30867OOB|1|P:2YU9|1|R = 0.30617OOB|1|P:1R9T|1|R = 0.37068B3F|1|P:9BVT|1|X = 0.37838B3F|1|P:7Z2Z|1|R = 0.35708B3F|1|P:2NVQ|1|R = 0.15118B3F|1|P:7OO3|1|P = 0.05708B3F|1|P:7OOB|1|P = 0.06358B3F|1|P:8B3F|1|P = 08B3F|1|P:8B3D|1|P = 0.00038B3F|1|P:8TVY|1|R = 0.12018B3F|1|P:8TUG|1|R = 0.14368B3F|1|P:6UPZ|1|R = 0.27368B3F|1|P:7KEE|1|R = 0.20578B3F|1|P:2E2I|1|R = 0.28178B3F|1|P:2YU9|1|R = 0.28548B3F|1|P:1R9T|1|R = 0.34078B3D|1|P:9BVT|1|X = 0.37838B3D|1|P:7Z2Z|1|R = 0.35708B3D|1|P:2NVQ|1|R = 0.15118B3D|1|P:7OO3|1|P = 0.05708B3D|1|P:7OOB|1|P = 0.06358B3D|1|P:8B3F|1|P = 0.00038B3D|1|P:8B3D|1|P = 08B3D|1|P:8TVY|1|R = 0.12028B3D|1|P:8TUG|1|R = 0.14378B3D|1|P:6UPZ|1|R = 0.27358B3D|1|P:7KEE|1|R = 0.20578B3D|1|P:2E2I|1|R = 0.28178B3D|1|P:2YU9|1|R = 0.28548B3D|1|P:1R9T|1|R = 0.34078TVY|1|R:9BVT|1|X = 0.35948TVY|1|R:7Z2Z|1|R = 0.56548TVY|1|R:2NVQ|1|R = 0.21548TVY|1|R:7OO3|1|P = 0.14228TVY|1|R:7OOB|1|P = 0.13678TVY|1|R:8B3F|1|P = 0.12018TVY|1|R:8B3D|1|P = 0.12028TVY|1|R:8TVY|1|R = 08TVY|1|R:8TUG|1|R = 0.10698TVY|1|R:6UPZ|1|R = 0.30368TVY|1|R:7KEE|1|R = 0.22638TVY|1|R:2E2I|1|R = 0.32208TVY|1|R:2YU9|1|R = 0.33318TVY|1|R:1R9T|1|R = 0.37308TUG|1|R:9BVT|1|X = 0.38268TUG|1|R:7Z2Z|1|R = 0.60968TUG|1|R:2NVQ|1|R = 0.21868TUG|1|R:7OO3|1|P = 0.15108TUG|1|R:7OOB|1|P = 0.14798TUG|1|R:8B3F|1|P = 0.14368TUG|1|R:8B3D|1|P = 0.14378TUG|1|R:8TVY|1|R = 0.10698TUG|1|R:8TUG|1|R = 08TUG|1|R:6UPZ|1|R = 0.29998TUG|1|R:7KEE|1|R = 0.25358TUG|1|R:2E2I|1|R = 0.32508TUG|1|R:2YU9|1|R = 0.33418TUG|1|R:1R9T|1|R = 0.38956UPZ|1|R:9BVT|1|X = 0.47826UPZ|1|R:7Z2Z|1|R = 0.72926UPZ|1|R:2NVQ|1|R = 0.27226UPZ|1|R:7OO3|1|P = 0.27086UPZ|1|R:7OOB|1|P = 0.29686UPZ|1|R:8B3F|1|P = 0.27366UPZ|1|R:8B3D|1|P = 0.27356UPZ|1|R:8TVY|1|R = 0.30366UPZ|1|R:8TUG|1|R = 0.29996UPZ|1|R:6UPZ|1|R = 06UPZ|1|R:7KEE|1|R = 0.23966UPZ|1|R:2E2I|1|R = 0.31866UPZ|1|R:2YU9|1|R = 0.31086UPZ|1|R:1R9T|1|R = 0.35757KEE|1|R:9BVT|1|X = 0.38887KEE|1|R:7Z2Z|1|R = 0.44337KEE|1|R:2NVQ|1|R = 0.18817KEE|1|R:7OO3|1|P = 0.21017KEE|1|R:7OOB|1|P = 0.24317KEE|1|R:8B3F|1|P = 0.20577KEE|1|R:8B3D|1|P = 0.20577KEE|1|R:8TVY|1|R = 0.22637KEE|1|R:8TUG|1|R = 0.25357KEE|1|R:6UPZ|1|R = 0.23967KEE|1|R:7KEE|1|R = 07KEE|1|R:2E2I|1|R = 0.19587KEE|1|R:2YU9|1|R = 0.21517KEE|1|R:1R9T|1|R = 0.25552E2I|1|R:9BVT|1|X = 0.39412E2I|1|R:7Z2Z|1|R = 0.35432E2I|1|R:2NVQ|1|R = 0.19982E2I|1|R:7OO3|1|P = 0.27712E2I|1|R:7OOB|1|P = 0.30862E2I|1|R:8B3F|1|P = 0.28172E2I|1|R:8B3D|1|P = 0.28172E2I|1|R:8TVY|1|R = 0.32202E2I|1|R:8TUG|1|R = 0.32502E2I|1|R:6UPZ|1|R = 0.31862E2I|1|R:7KEE|1|R = 0.19582E2I|1|R:2E2I|1|R = 02E2I|1|R:2YU9|1|R = 0.17152E2I|1|R:1R9T|1|R = 0.28002YU9|1|R:9BVT|1|X = 0.40602YU9|1|R:7Z2Z|1|R = 0.41262YU9|1|R:2NVQ|1|R = 0.20342YU9|1|R:7OO3|1|P = 0.26752YU9|1|R:7OOB|1|P = 0.30612YU9|1|R:8B3F|1|P = 0.28542YU9|1|R:8B3D|1|P = 0.28542YU9|1|R:8TVY|1|R = 0.33312YU9|1|R:8TUG|1|R = 0.33412YU9|1|R:6UPZ|1|R = 0.31082YU9|1|R:7KEE|1|R = 0.21512YU9|1|R:2E2I|1|R = 0.17152YU9|1|R:2YU9|1|R = 02YU9|1|R:1R9T|1|R = 0.25531R9T|1|R:9BVT|1|X = 0.39121R9T|1|R:7Z2Z|1|R = 0.45301R9T|1|R:2NVQ|1|R = 0.31161R9T|1|R:7OO3|1|P = 0.33661R9T|1|R:7OOB|1|P = 0.37061R9T|1|R:8B3F|1|P = 0.34071R9T|1|R:8B3D|1|P = 0.34071R9T|1|R:8TVY|1|R = 0.37301R9T|1|R:8TUG|1|R = 0.38951R9T|1|R:6UPZ|1|R = 0.35751R9T|1|R:7KEE|1|R = 0.25551R9T|1|R:2E2I|1|R = 0.28001R9T|1|R:2YU9|1|R = 0.25531R9T|1|R:1R9T|1|R = 09BVT|1|X7Z2Z|1|R2NVQ|1|R7OO3|1|P7OOB|1|P8B3F|1|P8B3D|1|P8TVY|1|R8TUG|1|R6UPZ|1|R7KEE|1|R2E2I|1|R2YU9|1|R1R9T|1|RDiscrepancy0.000.200.400.60

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