PDB-8za0: Crystal structure of OR4K15 ribozyme

ID or keywords:

Entry

Database: PDB / ID: 8za0

Title

Crystal structure of OR4K15 ribozyme

Components

(RNA (5'-R(*UP*CP*UP*GP*GP*GP*CP*CP*AP*GP*GP*CP*AP*GP*G)-3')) x 2

Keywords

RNA / ribozyme / OR4K15

Function / homology

RNA / RNA (> 10)

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96 Å

Authors

Ren, Y. / Huang, L.

Funding support

China, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2025
Title: A general strategy for engineering GU base pairs to facilitate RNA crystallization.
Authors: Ren, Y. / Lin, X. / Liao, W. / Peng, X. / Deng, J. / Zhang, Z. / Zhan, J. / Zhou, Y. / Westhof, E. / Lilley, D.M.J. / Wang, J. / Huang, L.

History

Deposition	Apr 24, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Mar 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8za0.cif.gz	136.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8za0.ent.gz	88.4 KB	Display	PDB format
PDBx/mmJSON format	8za0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/za/8za0 ftp://data.pdbj.org/pub/pdb/validation_reports/za/8za0	HTTPS FTP

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Related structure data

Related structure data	8k7wC 8kebC 8z8qC 8z8uC 8z9kC 8za4C 8zauC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #65 - May 2005 Self-splicing RNA similarity (2) #87 - Mar 2007 Zinc Fingers similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #227 - Nov 2018 Telomerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (2)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: RNA (5'-R(*UP*CP*UP*GP*GP*GP*CP*CP*AP*GP*GP*CP*AP*GP*G)-3')

B: RNA (5'-R(*UP*CP*UP*GP*GP*GP*CP*CP*AP*GP*GP*CP*AP*GP*G)-3')

C: RNA (5'-R(*UP*CP*UP*GP*GP*GP*CP*CP*AP*GP*GP*CP*AP*GP*G)-3')

D: RNA (5'-R(*UP*CP*UP*GP*GP*GP*CP*CP*AP*GP*GP*CP*AP*GP*G)-3')

E: RNA (5'-R(*UP*CP*UP*GP*GP*GP*CP*CP*AP*GP*GP*CP*AP*GP*G)-3')

F: RNA (5'-R(*UP*CP*UP*GP*GP*GP*CP*CP*AP*GP*GP*CP*AP*GP*G)-3')

hetero molecules

29.9 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	72.082, 36.570, 113.940
Angle α, β, γ (deg.)	90.000, 91.290, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: RNA chain	RNA (5'-R(UPCPUPGPGPGPCPCPAPGPGPCPAPGPG)-3') Mass: 4862.954 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens* (human)
#2: RNA chain	RNA (5'-R(UPCPUPGPGPGPCPCPAPGPGPCPAPGPG)-3') Mass: 5056.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens* (human)
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium Cacodylate pH 5.6 1.5 M Sodium Acetate trihydrate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.978557 Å
Detector	Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Aug 29, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978557 Å / Relative weight: 1
Reflection	Resolution: 1.96→56.96 Å / Num. obs: 21733 / % possible obs: 100 % / Redundancy: 6.1 % / B_iso Wilson estimate: 32.09 Å² / CC_1/2: 0.995 / Net I/σ(I): 5.9
Reflection shell	Resolution: 1.96→2.01 Å / Num. unique obs: 1609 / CC_1/2: 0.657

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
PHENIX	1.20.1_4487	refinement
PROCOR		data reduction
PROCOR		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.96→56.96 Å / SU ML: 0.217 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8609
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2298	1068	4.96 %
R_work	0.2031	20484	-
obs	0.2045	21552	99.16 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 33.78 Å²

Refinement step

Cycle: LAST / Resolution: 1.96→56.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	1965	5	145	2115

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0157	2193
X-RAY DIFFRACTION	f_angle_d	2.0869	3408
X-RAY DIFFRACTION	f_chiral_restr	0.0902	456
X-RAY DIFFRACTION	f_plane_restr	0.0149	93
X-RAY DIFFRACTION	f_dihedral_angle_d	10.6867	1086

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.96-2.05	0.2997	143	0.3057	2538	X-RAY DIFFRACTION	99.55
2.05-2.16	0.3411	151	0.2776	2521	X-RAY DIFFRACTION	99.66
2.16-2.29	0.2853	112	0.2757	2580	X-RAY DIFFRACTION	99.7
2.29-2.47	0.3002	132	0.2576	2528	X-RAY DIFFRACTION	99.44
2.47-2.72	0.3183	121	0.265	2600	X-RAY DIFFRACTION	99.71
2.72-3.11	0.2732	122	0.2324	2519	X-RAY DIFFRACTION	97.2
3.11-3.92	0.1852	140	0.1563	2543	X-RAY DIFFRACTION	98.64
3.92-56.96	0.1687	147	0.1514	2655	X-RAY DIFFRACTION	99.4

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.0724428409877	-0.239386667833	-1.31764033238	0.386715833611	-0.0733737593754	4.89580237333	-0.05687585116	-0.157927871968	0.01635973301	0.0771227233494	0.0520895241136	0.00883875359348	0.407076945766	0.336081624169	-0.00898880089759	0.249250385793	0.0335806041821	0.00456595921993	0.344432014589	0.0303967669347	0.209936484388	-15.877691802	-0.701516111358	21.5080161636
2	3.80124246922	-0.0551212091276	-0.00795957758312	3.19764203812	-2.83577321151	5.53556071551	0.0902215102705	-0.0519246740493	-0.173865869418	-0.159549313614	-0.156039036092	0.655188210548	0.703884175026	-0.0117535011168	0.0592980997354	0.324684569239	0.0123358249881	0.0641299673865	0.220692869741	-0.0329386204722	0.208723463842	-21.6482386869	-4.3590856368	30.9792616336
3	3.33501714504	-0.379355518584	1.78771652234	3.34751340453	-1.67563287999	1.60898409993	0.42053653418	0.0451845117692	0.0535464555723	-0.316755617608	0.0566549805951	-0.388438971401	0.104589150546	0.163234711967	-0.435556154429	0.498962289472	0.00536431220528	0.00563810509788	0.40263471921	-0.00202727600677	0.214960444397	-15.6217979161	2.81469504116	19.5772296998
4	2.47693171087	0.533912108797	-0.971892421887	3.39906986707	-4.55649384966	6.32423403023	0.210699365985	0.222476017249	-0.0317453824751	-0.391008432173	0.168610535901	0.228576661998	0.308705050797	0.0977043187953	-0.315247131733	0.268948616697	-0.0142649643367	-0.0452778836449	0.332118500577	-0.00155403425773	0.205668892328	-19.1641206389	-1.97907453658	4.65369227734
5	0.0819972998784	-0.234251613107	1.06423466171	0.362017245688	-1.72735123981	4.9280180853	0.081119112039	0.0463004843092	0.0447700776506	0.122532183793	0.118776808377	0.0919245445904	-0.3476312746	-0.165965896167	-0.241051225275	0.321260775003	0.0618681754461	0.0122305677052	0.415858879224	0.0291810108268	0.25801727751	-30.3198468906	15.241538857	16.6414182956
6	3.88947722885	-0.519803946601	-1.42912166867	1.69376900018	-0.166257707824	3.4339678372	-0.160337130837	-0.789156809258	0.483870737013	0.183175858825	0.0522201666334	0.0961128428562	-0.205283907187	0.842310508199	0.094970435838	0.190238717629	-0.0132807494702	-0.0666351740064	0.272155218804	0.0433764743355	0.244924779473	-30.7038987101	21.7170053359	6.81122602157
7	2.10669416644	-0.0172684870718	-1.27086994606	2.02208060014	-0.0995734535333	0.853200750687	-0.0237991858937	0.151168345294	-0.0824589654939	0.0885042941833	0.153562117231	-0.164406698701	-0.204131026775	0.12187681033	-0.163544921917	0.357513198423	0.00734270509155	-0.00331491972889	0.497015361815	0.0195439080734	0.216599372501	-32.9590209025	12.9105325769	18.6879985425
8	7.59152662569	3.31066215488	-2.15421688206	6.29513520049	-2.45239971123	4.96176708878	0.259281610456	-0.507659313785	0.570775848544	0.349722924225	0.241403474167	0.307331445419	-0.750555098336	-0.213170701497	-0.471185112309	0.373351443536	0.0485394693719	0.0563980937374	0.313116366586	-0.0154823819478	0.20866859858	-31.1404308097	18.8664386299	33.4603079585
9	-0.0227055312938	-0.22527770761	-0.909412552372	-0.559186307946	0.501222835858	7.79991619206	0.0895208774386	0.0528913077756	-0.124531274646	-0.0359644176183	-0.033053813184	0.0513116371715	0.371225991806	-0.580847032692	-0.093348729651	0.381321729878	-0.0666391551534	-0.0320354172856	0.290212835081	0.024895473094	0.247509318181	-24.974904355	7.85711214524	54.7307994238
10	5.46661988089	-1.51238754729	3.08391740391	1.95809217386	-1.77117429659	4.12079006522	-0.192166619485	-0.484759391059	-0.768416672214	0.454807550913	0.281234177439	0.248250759891	-0.191540835119	-0.153948658285	-0.0890524892207	0.248487700033	-0.00571862077505	-0.020625637158	0.310295930046	-0.0300456170539	0.261190923528	-28.5331141461	3.97124365615	44.7324527633
11	1.4050050837	-0.561760718171	-0.0435890821131	1.51770127834	0.0365587854947	-0.0212979214329	0.265289047969	-0.438846897717	0.229045518291	0.129553144563	-0.071631959132	-0.172178222326	-0.00708629497314	0.342627484449	-0.0958382135012	0.469902725116	0.0285191473986	0.042921455663	0.379365147789	-0.0207812960504	0.204723273779	-20.749961581	7.07869202304	56.932713204
12	7.10472389412	-2.12422796542	1.62647511112	5.85270940292	-0.538225929453	3.55670842235	0.0339815615441	-0.0441734669115	-0.0992984961408	0.109998195534	0.0795767847182	0.0831198229437	0.411100708499	-0.427058437881	-0.031275259087	0.308780950207	-0.0287888601	0.0271831286915	0.344606533693	0.0160180279347	0.23359915219	-28.9356051812	6.05546488209	71.7785523515

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 15 )	A	A	1 - 15
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 1 through 5 )	B	B	1 - 5
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 6 through 10 )	B	B	6 - 10
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 11 through 16 )	B	B	11 - 16
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 1 through 15 )	C	C	1 - 15
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 1 through 5 )	D	D	1 - 5
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 6 through 10 )	D	D	6 - 10
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 11 through 16 )	D	D	11 - 16
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 1 through 15 )	E	E	1 - 15
10	X-RAY DIFFRACTION	10	chain 'F' and (resid 1 through 5 )	F	F	1 - 5
11	X-RAY DIFFRACTION	11	chain 'F' and (resid 6 through 10 )	F	F	6 - 10
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 11 through 16 )	F	F	11 - 16

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