PDB-3pla: Crystal structure of a catalytically active substrate-bound box C...

ID or keywords:

Entry

Database: PDB / ID: 3pla

Title

Crystal structure of a catalytically active substrate-bound box C/D RNP from Sulfolobus solfataricus

Components

50S ribosomal protein L7Ae
C/D guide RNA
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Pre mRNA splicing protein
RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3')

Keywords

TRANSFERASE/RNA / RNA-binding / METHYLTRANSFERASE / SAM / Box C/D RNA / Guide RNA / RNA-Protein complex / TRANSFERASE-RNA complex

Function / homology

Function and homology information

histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / rRNA methylation / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases ...
Similarity search - Function

Biological species

Sulfolobus solfataricus (archaea)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.15 Å

Authors

Lin, J. / Lai, S. / Jia, R. / Xu, A. / Zhang, L. / Lu, J. / Ye, K.

Citation

Journal: Nature / Year: 2011
Title: Structural basis for site-specific ribose methylation by box C/D RNA protein complexes.
Authors: Lin, J. / Lai, S. / Jia, R. / Xu, A. / Zhang, L. / Lu, J. / Ye, K.

History

Deposition	Nov 15, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jan 26, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 17, 2018	Group: Data collection / Database references / Source and taxonomy Category: citation / pdbx_entity_src_syn Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3pla.cif.gz	989.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3pla.ent.gz	823.4 KB	Display	PDB format
PDBx/mmJSON format	3pla.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3pla_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	3pla_full_validation.pdf.gz	1.2 MB	Display
Data in XML	3pla_validation.xml.gz	79.9 KB	Display
Data in CIF	3pla_validation.cif.gz	109.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pl/3pla ftp://data.pdbj.org/pub/pdb/validation_reports/pl/3pla	HTTPS FTP

-
Related structure data

Related structure data	3icxS 3id5S 3id6S S: Starting model for refinement
Similar structure data	5gin-1 5gio-1 5gvc-d 6ske-1 6ske-2 4ajw-d 5te8-d 2wp8-d 5gip-1 6ydu-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (7) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #260 - Aug 2021 Ribonuclease P similarity (7) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome 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 (7) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #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) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #161 - May 2013 Ricin similarity (6) #266 - Feb 2022 Oligosaccharyltransferase similarity (4) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E 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 (7)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (7)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
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 (7)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#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)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#161 - May 2013
Ricin
similarity (6)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (4)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
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: Pre mRNA splicing protein

B: Pre mRNA splicing protein

C: 50S ribosomal protein L7Ae

D: 50S ribosomal protein L7Ae

E: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase

F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase

G: C/D guide RNA

H: C/D guide RNA

I: RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3')

J: RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3')

K: Pre mRNA splicing protein

L: 50S ribosomal protein L7Ae

M: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase

N: C/D guide RNA

O: RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3')

hetero molecules

303 kDa, 15 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pre mRNA splicing protein

B: Pre mRNA splicing protein

C: 50S ribosomal protein L7Ae

D: 50S ribosomal protein L7Ae

E: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase

F: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase

G: C/D guide RNA

H: C/D guide RNA

I: RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3')

J: RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3')

hetero molecules

defined by author&software
202 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

K: Pre mRNA splicing protein

L: 50S ribosomal protein L7Ae

M: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase

N: C/D guide RNA

O: RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3')

hetero molecules

K: Pre mRNA splicing protein

L: 50S ribosomal protein L7Ae

M: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase

N: C/D guide RNA

O: RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3')

hetero molecules

defined by author&software
202 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	241.199, 241.199, 145.408
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1 - 132
2	1	1	1	B	1 - 132
3	1	1	1	K	1 - 132
1	1	2	1	A	133 - 185
2	1	2	1	B	133 - 185
3	1	2	1	K	133 - 185
1	1	3	1	A	262 - 353
2	1	3	1	B	262 - 353
3	1	3	1	K	262 - 353
1	1	4	1	C	7 - 128
2	1	4	1	D	7 - 128
3	1	4	1	L	7 - 128
1	1	5	1	E	5 - 301
2	1	5	1	F	5 - 301
3	1	5	1	M	5 - 301
1	1	6	1	G	10 - 17
2	1	6	1	H	10 - 17
3	1	6	1	N	10 - 17
1	1	7	1	G	18 - 27
2	1	7	1	H	18 - 27
3	1	7	1	N	18 - 27
1	1	8	1	G	28 - 32
2	1	8	1	H	28 - 32
3	1	8	1	N	28 - 32
1	1	9	1	I	1 - 10
2	1	9	1	J	1 - 10
3	1	9	1	O	1 - 10
1	1	10	1	A	359 - 377
2	1	10	1	B	359 - 377
3	1	10	1	K	359 - 377
1	1	11	1	A	207 - 261
2	1	11	1	B	207 - 261
3	1	11	1	K	207 - 261

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11

-
Protein , 3 types, 9 molecules ABKCDLEFM

#1: Protein	Pre mRNA splicing protein / NOP5 Mass: 44168.531 Da / Num. of mol.: 3 / Fragment: UNP residues 1-380 / Mutation: M2V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO0939 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/RIL+ / References: UniProt: Q97ZH3
#2: Protein	50S ribosomal protein L7Ae Mass: 14075.301 Da / Num. of mol.: 3 / Mutation: N2D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: 98/2 / Gene: rpl7ae, Ssol_1068 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/RIL+ / References: UniProt: D0KRE2
#3: Protein	Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase / FIB Mass: 26439.375 Da / Num. of mol.: 3 / Mutation: S2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: flpA, SSO0940, C33_014 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/RIL+ References: UniProt: P58032, Transferases; Transferring one-carbon groups; Methyltransferases

-
RNA chain , 2 types, 6 molecules GHNIJO

#4: RNA chain	C/D guide RNA Mass: 12852.657 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: In vitro transcription / Source: (synth.) synthetic construct (others)
#5: RNA chain	RNA (5'-R(CPCPAPUPGPAPGPUPGPU)-3') Mass: 3177.932 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Chemical synthesis / Source: (synth.) synthetic construct (others)

-
Non-polymers , 1 types, 3 molecules

#6: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.5 Å³/Da / Density % sol: 64.85 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.0M (NH4)2SO4, 2% PEG 400, 10mM MgCl2, 0.1M HEPES-Na (pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 15, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9789 Å / Relative weight: 1
Reflection	Resolution: 3.15→20 Å / Num. obs: 70682 / % possible obs: 95.1 % / Redundancy: 4.3 % / R_merge(I) obs: 0.095 / Net I/σ(I): 16.3
Reflection shell	Resolution: 3.15→3.2 Å / Redundancy: 4 % / R_merge(I) obs: 0.536 / Mean I/σ(I) obs: 2.3 / % possible all: 94.4

-
Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3ICX, 3ID6, 3ID5

3icx

3id6

3id5

Resolution: 3.15→19.91 Å / Cor.coef. F_o:F_c: 0.914 / Cor.coef. F_o:F_c free: 0.89 / SU B: 52.016 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R Free: 0.495 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27761	3540	5 %	RANDOM
R_work	0.24776	-	-	-
obs	0.24928	66836	95.11 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 88.687 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.18 Å²	0 Å²	0 Å²
2-	-	-1.18 Å²	0 Å²
3-	-	-	2.36 Å²

Refinement step

Cycle: LAST / Resolution: 3.15→19.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17247	2721	78	0	20046

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	20649
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.324	2.154	28505
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.538	5	2163
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.77	24.366	804
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.228	15	3282
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.803	15	129
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	3352
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	14372
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.698	1.5	10836
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.066	2	17508
X-RAY DIFFRACTION	r_scbond_it	0.92	3	9813
X-RAY DIFFRACTION	r_scangle_it	1.599	4.5	10997
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1059	TIGHT POSITIONAL	0.06	0.1
1	1	B	1059	TIGHT POSITIONAL	0.05	0.1
1	1	K	1059	TIGHT POSITIONAL	0.05	0.1
1	1	A	1059	TIGHT THERMAL	11.52	40
1	1	B	1059	TIGHT THERMAL	8.17	40
1	1	K	1059	TIGHT THERMAL	19.28	40
2	1	A	448	TIGHT POSITIONAL	0.07	0.1
2	1	B	448	TIGHT POSITIONAL	0.07	0.1
2	1	K	448	TIGHT POSITIONAL	0.07	0.1
2	1	A	448	TIGHT THERMAL	5.73	40
2	1	B	448	TIGHT THERMAL	7.62	40
2	1	K	448	TIGHT THERMAL	11.95	40
3	1	A	677	TIGHT POSITIONAL	0.07	0.1
3	2	B	677	TIGHT POSITIONAL	0.08	0.1
3	3	K	677	TIGHT POSITIONAL	0.07	0.1
3	1	A	677	TIGHT THERMAL	3.87	40
3	2	B	677	TIGHT THERMAL	18.25	40
3	3	K	677	TIGHT THERMAL	16.97	40
4	1	C	927	TIGHT POSITIONAL	0.06	0.1
4	1	D	927	TIGHT POSITIONAL	0.07	0.1
4	1	L	927	TIGHT POSITIONAL	0.05	0.1
4	1	C	927	TIGHT THERMAL	3.57	40
4	1	D	927	TIGHT THERMAL	20.91	40
4	1	L	927	TIGHT THERMAL	21.12	40
5	1	E	1855	TIGHT POSITIONAL	0.08	0.1
5	1	F	1855	TIGHT POSITIONAL	0.07	0.1
5	1	M	1855	TIGHT POSITIONAL	0.06	0.1
5	1	E	1855	TIGHT THERMAL	15.73	40
5	1	F	1855	TIGHT THERMAL	6.94	40
5	1	M	1855	TIGHT THERMAL	21.87	40
6	1	G	175	TIGHT POSITIONAL	0.11	0.1
6	1	H	175	TIGHT POSITIONAL	0.18	0.1
6	1	N	175	TIGHT POSITIONAL	0.1	0.1
6	1	G	175	TIGHT THERMAL	23.64	40
6	1	H	175	TIGHT THERMAL	3.95	40
6	1	N	175	TIGHT THERMAL	20.26	40
7	1	G	212	TIGHT POSITIONAL	0.16	0.1
7	1	H	212	TIGHT POSITIONAL	0.29	0.1
7	1	N	212	TIGHT POSITIONAL	0.16	0.1
7	1	G	212	TIGHT THERMAL	12.03	40
7	1	H	212	TIGHT THERMAL	7.76	40
7	1	N	212	TIGHT THERMAL	17.16	40
8	1	G	105	TIGHT POSITIONAL	0.13	0.1
8	1	H	105	TIGHT POSITIONAL	0.24	0.1
8	1	N	105	TIGHT POSITIONAL	0.13	0.1
8	1	G	105	TIGHT THERMAL	5.29	40
8	1	H	105	TIGHT THERMAL	23	40
8	1	N	105	TIGHT THERMAL	20.88	40
9	1	C	210	TIGHT POSITIONAL	0.08	0.1
9	1	I	210	TIGHT POSITIONAL	0.08	0.1
9	1	J	210	TIGHT POSITIONAL	0.07	0.1
9	1	C	210	TIGHT THERMAL	13.95	40
9	1	I	210	TIGHT THERMAL	6.2	40
9	1	J	210	TIGHT THERMAL	19.69	40
10	1	A	160	TIGHT POSITIONAL	0.06	0.1
10	1	B	160	TIGHT POSITIONAL	0.08	0.1
10	1	K	160	TIGHT POSITIONAL	0.06	0.1
10	1	A	160	TIGHT THERMAL	8.16	40
10	1	B	160	TIGHT THERMAL	23.17	40
10	1	K	160	TIGHT THERMAL	15.12	40
11	1	A	439	TIGHT POSITIONAL	0.08	0.1
11	1	B	439	TIGHT POSITIONAL	0.07	0.1
11	1	K	439	TIGHT POSITIONAL	0.07	0.1
11	1	A	439	TIGHT THERMAL	8.55	40
11	1	B	439	TIGHT THERMAL	8.77	40
11	1	K	439	TIGHT THERMAL	10.33	40

LS refinement shell

Resolution: 3.15→3.23 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.344	276	-
R_work	0.308	4702	-
obs	-	-	93.68 %

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	2.9017	0.04	-0.4967	2.2481	0.29	0.5957	0.0607	-0.2267	-0.1323	0.1084	-0.034	0.2041	0.1228	-0.2341	-0.0267	0.1841	-0.0814	0.0653	0.2307	0.0925	0.1125	59.485	-34.4832	30.0042
2	2.5141	-0.0778	-0.2524	0.304	0.0143	0.2206	0.0309	0.0963	-0.2482	0.1028	0.0532	0.0205	0.144	0.0156	-0.0841	0.167	0.0375	-0.076	0.0771	0.0177	0.1099	121.9036	-46.0274	24.6997
3	1.9821	0.3328	-0.6859	1.339	0.3617	1.8812	0.1013	0.0658	-0.4316	0.1323	-0.0852	0.0338	0.0796	0.0353	-0.0161	0.097	-0.0107	-0.0671	0.017	-0.034	0.2136	95.1081	-55.7843	9.9496
4	2.5332	-0.1391	-0.1867	2.9214	0.889	0.5322	0.1289	0.2379	-0.114	-0.0739	-0.0615	-0.5317	-0.0202	0.1286	-0.0674	0.0592	0.105	-0.0105	0.271	0.0183	0.1407	159.3994	-33.4861	-3.5282
5	2.263	0.5372	-0.8159	0.382	-0.3875	0.8933	0.1072	-0.1697	-0.0649	0.2231	-0.0015	-0.0139	-0.009	-0.0223	-0.1057	0.2594	0.0023	-0.0385	0.1072	0.04	0.049	107.6665	-30.3476	33.8177
6	2.0025	0.0645	0.1974	0.9839	-0.2602	0.9859	-0.0059	-0.0887	0.0369	0.0661	-0.0239	-0.0245	0.0159	-0.038	0.0298	0.1313	0.021	-0.0317	0.095	-0.0124	0.0095	122.284	-11.1151	12.4085
7	0.9314	0.0114	-1.0445	0.7762	-0.6795	2.0393	-0.0353	0.2954	-0.2579	-0.2	0.0119	0.0541	0.0886	-0.1686	0.0233	0.17	0.0238	-0.0031	0.3694	-0.3559	0.3625	161.3264	-108.3823	-48.4201
8	0.482	-0.2205	-0.109	0.7929	0.9551	2.3961	-0.0958	0.0187	-0.0068	-0.0205	-0.1	0.2151	-0.1545	0.0139	0.1958	0.1291	0.0788	0.0258	0.1182	-0.0521	0.2211	152.6042	-73.644	4.4724
9	2.2805	-0.7932	-0.6988	1.8719	-0.181	1.7993	-0.0647	0.1773	-0.1023	-0.1094	-0.011	0.1914	-0.1241	-0.1618	0.0757	0.0722	0.0525	-0.0681	0.1391	-0.1633	0.249	134.5278	-83.6107	-20.3678
10	3.1431	-0.1686	-0.7096	1.7676	0.1648	1.8001	-0.0624	0.2687	-0.4926	0.1076	0.1545	0.2466	0.137	-0.2059	-0.0921	0.1663	-0.1053	-0.043	0.1235	0.0079	0.2776	68.9543	-56.183	5.4106
11	1.8536	0.0283	-0.2605	1.6708	0.2201	2.8803	0.0486	0.1388	0.158	-0.0692	0.0086	-0.1615	0.0078	0.1428	-0.0572	0.0225	-0.02	-0.0048	0.1269	0.0394	0.0439	140.8944	-4.9095	-5.3798
12	1.8335	0.7103	-0.4184	2.1565	0.2031	1.7183	-0.163	0.2706	0.009	-0.4119	0.1037	0.1291	0.0147	-0.2581	0.0593	0.1235	0.0731	-0.1265	0.3096	-0.2501	0.2578	129.9118	-96.9945	-42.8492
13	1.3685	0.1415	0.0867	1.2395	0.1602	1.155	-0.0197	-0.0133	0.0399	0.0704	0.0936	0.1279	-0.0386	-0.077	-0.0739	0.1146	-0.0438	0.0495	0.1219	0.054	0.0749	77.4022	-19.1364	14.5207
14	1.207	-0.06	0.14	1.7426	0.0866	0.6535	0.0469	0.1732	-0.1656	-0.1434	-0.0056	-0.0591	0.0626	0.1055	-0.0413	0.0915	0.112	-0.0288	0.1706	-0.0627	0.0357	133.6333	-42.7109	-10.8628
15	0.9189	0.3499	0.1114	0.9416	-0.721	1.6531	0.001	0.0582	-0.3075	-0.1552	-0.0197	0.0057	0.1608	-0.0232	0.0186	0.0925	0.0556	-0.0144	0.1556	-0.2224	0.4797	155.3098	-118.9887	-22.6709
16	0.6268	-0.5947	0.5087	1.7654	-0.9417	0.5897	-0.1671	-0.0597	-0.0285	0.2203	0.1565	-0.0248	-0.171	-0.0827	0.0107	0.2389	0.0889	-0.0363	0.1152	-0.0145	0.0562	117.9286	20.6778	4.4724
17	1.7859	0.117	0.5015	0.0331	-0.0279	1.3464	-0.0137	0.1801	0.1725	0.02	-0.0043	0.0434	-0.125	0.079	0.018	0.1493	-0.0147	-0.0176	0.1217	0.0386	0.0881	120.9379	-3.8592	2.2183
18	0.6499	-0.0838	0.1587	0.1018	-0.2222	0.495	0.053	-0.039	-0.103	0.0019	0.0229	0.0249	0.0099	-0.04	-0.0759	0.16	-0.0473	-0.0007	0.102	-0.0082	0.1303	97.8578	-28.0861	14.2046
19	1.2622	0.843	0.2878	1.2507	-0.6523	1.5301	0.0917	0.154	-0.2518	-0.2011	0.0846	0.1277	0.2063	0.0743	-0.1763	0.2078	-0.0523	-0.1243	0.0928	-0.1113	0.3691	89.2713	-57.3737	-1.1422
20	0.1466	-0.1468	0.0068	0.1483	-0.014	0.0384	0.058	0.0582	-0.1239	-0.0604	-0.0677	0.122	0.0477	0.0679	0.0097	0.1833	0.0169	-0.0308	0.1952	-0.031	0.1081	118.3639	-37.8606	4.6724
21	43.4006	-2.4188	-2.9949	15.3917	-2.1158	2.2819	-0.0088	-1.1969	-2.5905	-0.2726	-0.5266	-0.1249	0.3869	-0.071	0.5354	0.34	-0.0282	0.0606	0.2464	-0.126	0.3883	90.8055	-69.6793	-6.9248
22	35.2152	-26.8294	9.6138	54.2041	-21.0325	8.1909	0.3354	-0.8893	-0.8994	0.9412	0.2686	1.4036	-0.3852	-0.0868	-0.6041	0.5823	0.2519	0.1616	0.2532	-0.0714	0.3839	167.3122	-127.538	31.5869
23	0.6382	0.1625	-0.1044	0.2008	0.0518	0.0562	-0.045	0.035	-0.2668	0.0019	-0.1026	0.1314	0.0246	-0.0536	0.1476	0.2232	0.1339	0.1275	0.1776	-0.1005	0.4651	144.3064	-109.9049	7.0706
24	0.1237	0.0832	-0.0506	0.0836	-0.0388	0.022	0.0154	0.0014	-0.0434	0.04	-0.01	0.0739	-0.0059	0.0097	-0.0054	0.1152	0.1091	0.0565	0.1693	-0.0944	0.4226	151.3689	-102.8407	-8.0878
25	23.6688	-24.9978	3.1972	28.6679	-5.6394	2.6993	0.0411	0.0361	0.184	-0.045	-0.1285	-0.1611	0.0351	0.084	0.0874	0.0838	0.0664	0.0463	0.2558	-0.3134	0.6365	111.4958	-79.5353	-25.3368

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 132
2	X-RAY DIFFRACTION	2	A	133 - 261
3	X-RAY DIFFRACTION	3	A	262 - 377
4	X-RAY DIFFRACTION	4	B	3 - 132
5	X-RAY DIFFRACTION	5	B	133 - 261
6	X-RAY DIFFRACTION	6	B	262 - 377
7	X-RAY DIFFRACTION	7	K	3 - 132
8	X-RAY DIFFRACTION	8	K	133 - 261
9	X-RAY DIFFRACTION	9	K	262 - 377
10	X-RAY DIFFRACTION	10	C	7 - 128
11	X-RAY DIFFRACTION	11	D	7 - 128
12	X-RAY DIFFRACTION	12	L	7 - 128
13	X-RAY DIFFRACTION	13	E	5 - 231
14	X-RAY DIFFRACTION	14	F	5 - 231
15	X-RAY DIFFRACTION	15	M	5 - 231
16	X-RAY DIFFRACTION	16	G	1 - 8
17	X-RAY DIFFRACTION	16	H	33 - 40
18	X-RAY DIFFRACTION	17	G	9 - 17
19	X-RAY DIFFRACTION	17	H	28 - 32
20	X-RAY DIFFRACTION	18	G	18 - 27
21	X-RAY DIFFRACTION	18	I	1 - 10
22	X-RAY DIFFRACTION	19	G	28 - 32
23	X-RAY DIFFRACTION	19	H	9 - 17
24	X-RAY DIFFRACTION	20	H	18 - 27
25	X-RAY DIFFRACTION	20	J	1 - 10
26	X-RAY DIFFRACTION	21	G	33 - 35
27	X-RAY DIFFRACTION	22	N	6 - 8
28	X-RAY DIFFRACTION	23	N	9 - 17
29	X-RAY DIFFRACTION	23	N	28 - 32
30	X-RAY DIFFRACTION	24	N	18 - 27
31	X-RAY DIFFRACTION	24	O	1 - 10
32	X-RAY DIFFRACTION	25	N	33 - 36

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 3 types, 9 molecules ABKCDLEFM

-
RNA chain , 2 types, 6 molecules GHNIJO

-
Non-polymers , 1 types, 3 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 3 types, 9 molecules ABKCDLEFM

-RNA chain , 2 types, 6 molecules GHNIJO

-Non-polymers , 1 types, 3 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 3 types, 9 molecules ABKCDLEFM

-
RNA chain , 2 types, 6 molecules GHNIJO

-
Non-polymers , 1 types, 3 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi