PDB-3blh: Crystal Structure of Human CDK9/cyclinT1

ID or keywords:

Entry

Database: PDB / ID: 3blh

Title

Crystal Structure of Human CDK9/cyclinT1

Components

Cell division protein kinase 9
Cyclin-T1

Keywords

TRANSCRIPTION / transcriptional CDK-cyclin complex / phosphorylated / Alternative splicing / ATP-binding / Kinase / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / Transcription regulation / Transferase / Acetylation / Cell cycle / Cell division / Coiled coil / Host-virus interaction

Function / homology

Function and homology information

P-TEFb complex / Interactions of Tat with host cellular proteins / nucleus localization / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / positive regulation of protein localization to chromatin / regulation of mRNA 3'-end processing / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 kinase activity ...P-TEFb complex / Interactions of Tat with host cellular proteins / nucleus localization / 7SK snRNA binding / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / positive regulation of protein localization to chromatin / regulation of mRNA 3'-end processing / RNA polymerase II CTD heptapeptide repeat Y1 kinase activity / RNA polymerase II CTD heptapeptide repeat S2 kinase activity / RNA polymerase II CTD heptapeptide repeat T4 kinase activity / RNA polymerase II CTD heptapeptide repeat S5 kinase activity / RNA polymerase II CTD heptapeptide repeat S7 kinase activity / transcription elongation factor activity / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / positive regulation of DNA-templated transcription, elongation / RNA polymerase binding / [RNA-polymerase]-subunit kinase / negative regulation of protein localization to chromatin / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription elongation-coupled chromatin remodeling / cellular response to cytokine stimulus / replication fork processing / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / cyclin-dependent kinase / Tat-mediated elongation of the HIV-1 transcript / cyclin-dependent protein serine/threonine kinase activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / regulation of DNA repair / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / transcription elongation factor complex / positive regulation of transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / molecular condensate scaffold activity / transcription coactivator binding / PML body / cytoplasmic ribonucleoprotein granule / kinase activity / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / cell population proliferation / protein kinase activity / transcription cis-regulatory region binding / regulation of cell cycle / protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / chromatin binding / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus / membrane / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.48 Å

Authors

Baumli, S. / Lolli, G. / Lowe, E.D. / Johnson, L.N.

Citation

Journal: Embo J. / Year: 2008
Title: The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation
Authors: Baumli, S. / Lolli, G. / Lowe, E.D. / Troiani, S. / Rusconi, L. / Bullock, A.N. / Debreczeni, J.E. / Knapp, S. / Johnson, L.N.

History

Deposition	Dec 11, 2007	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 1, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 10, 2021	Group: Database references / Derived calculations Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 1, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3blh.cif.gz	243.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3blh.ent.gz	196.6 KB	Display	PDB format
PDBx/mmJSON format	3blh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3blh_validation.pdf.gz	465.7 KB	Display	wwPDB validaton report
Full document	3blh_full_validation.pdf.gz	475.4 KB	Display
Data in XML	3blh_validation.xml.gz	23.6 KB	Display
Data in CIF	3blh_validation.cif.gz	32.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bl/3blh ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3blh	HTTPS FTP

-
Related structure data

Related structure data	2ivxC 3blqC 3blrC 1qmzS 2pk2S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3tnh-d 3blq-d 4f7s-d 3mia-d 4bcg-d 6b3e-2 6v7z-1 5cei-d 2y4i-d 3rgf-d 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	#236 - Aug 2019 Cyclin and Cyclin-dependent Kinase similarity (6) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (11) #67 - Jul 2005 TATA-Binding Protein similarity (5) #47 - Nov 2003 Simian Virus 40 similarity (3) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (2) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (2) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#236 - Aug 2019
Cyclin and Cyclin-dependent Kinase
similarity (6)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (11)
#67 - Jul 2005
TATA-Binding Protein
similarity (5)
#47 - Nov 2003
Simian Virus 40
similarity (3)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (2)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#213 - Sep 2017
Sirtuins
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (2)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (1)

Deposited unit

A: Cell division protein kinase 9

B: Cyclin-T1

hetero molecules

68.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	172.920, 172.920, 95.760
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3

#1: Protein	Cell division protein kinase 9 / Cyclin-dependent kinase 9 / Serine/threonine-protein kinase PITALRE / C-2K / Cell division cycle 2- ...Cyclin-dependent kinase 9 / Serine/threonine-protein kinase PITALRE / C-2K / Cell division cycle 2-like protein kinase 4 Mass: 38054.082 Da / Num. of mol.: 1 / Fragment: UNP Residues 2-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK9 / Plasmid: pVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein	Cyclin-T1 / CycT1 / Cyclin-T Mass: 30119.426 Da / Num. of mol.: 1 / Fragment: UNP Residues 2-259 / Mutation: Q77R, E96G, F241L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1 / Plasmid: pVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: O60563
#3: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.04 Å³/Da / Density % sol: 69.57 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris, 20% PEG 1000, 0.5M NaCl, 4mM TCEP, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.9756 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2007

Radiation

Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9756 Å / Relative weight: 1

Reflection

Resolution: 2.48→86.46 Å / Num. obs: 37491 / % possible obs: 99.1 % / Redundancy: 2.8 % / R_merge(I) obs: 0.063 / R_sym value: 0.063 / Net I/σ(I): 7.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.48-2.61	2.8	0.472	1.6	15467	5534	0.472	100
2.61-2.77	2.8	0.3	2.5	14609	5239	0.3	100
2.77-2.96	2.8	0.166	4.5	13705	4914	0.166	100
2.96-3.2	2.8	0.102	7.2	12722	4575	0.102	100
3.2-3.51	2.8	0.064	10	11593	4183	0.064	100
3.51-3.92	2.8	0.053	10.9	10524	3812	0.053	99.9
3.92-4.53	2.7	0.049	12.1	9188	3351	0.049	99.9
4.53-5.55	2.7	0.049	12.4	7671	2823	0.049	99.4
5.55-7.84	2.6	0.046	11.9	5530	2144	0.046	98.1
7.84-48.74	2.6	0.044	14.1	2350	916	0.044	76.5

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	48.73 Å
Translation	2.5 Å	48.73 Å

-
Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.004	data extraction
ProDC		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMZ FOR CHAIN A, PDB ENTRY 2PK2 FOR CHAIN B

1qmz

2pk2

Resolution: 2.48→48.726 Å / FOM work R set: 0.859 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ml

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.221	3600	4.98 %	RANDOM
R_work	0.179	-	-	-
obs	-	37490	95.5 %	-

Solvent computation

B_sol: 80.734 Å² / k_sol: 0.366 e/Å³

Displacement parameters

B_iso max: 196.83 Å² / B_iso mean: 74.79 Å² / B_iso min: 27.9 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.896 Å²	0 Å²	0 Å²
2-	-	-1.896 Å²	-0 Å²
3-	-	-	3.793 Å²

Refinement step

Cycle: LAST / Resolution: 2.48→48.726 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4454	0	8	139	4601

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.646	1
X-RAY DIFFRACTION	f_bond_d	0.005	1
X-RAY DIFFRACTION	f_chiral_restr	0.047	1
X-RAY DIFFRACTION	f_dihedral_angle_d	10.293	1
X-RAY DIFFRACTION	f_plane_restr	0.003	1
X-RAY DIFFRACTION	f_nbd_refined	4.062	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.48-2.486	0.299	494	X-RAY DIFFRACTION	137	92
2.486-2.492	0.31	532	X-RAY DIFFRACTION	137	90
2.492-2.498	0.284	469	X-RAY DIFFRACTION	137	90
2.498-2.505	0.32	521	X-RAY DIFFRACTION	137	92
2.505-2.511	0.288	487	X-RAY DIFFRACTION	137	90
2.511-2.517	0.292	490	X-RAY DIFFRACTION	137	88
2.517-2.524	0.273	509	X-RAY DIFFRACTION	137	90
2.524-2.53	0.282	516	X-RAY DIFFRACTION	137	93
2.53-2.537	0.274	477	X-RAY DIFFRACTION	137	90
2.537-2.543	0.271	519	X-RAY DIFFRACTION	137	93
2.543-2.55	0.271	487	X-RAY DIFFRACTION	137	92
2.55-2.557	0.269	581	X-RAY DIFFRACTION	137	94
2.557-2.564	0.269	462	X-RAY DIFFRACTION	137	92
2.564-2.571	0.26	539	X-RAY DIFFRACTION	137	93
2.571-2.578	0.25	523	X-RAY DIFFRACTION	137	92
2.578-2.585	0.267	507	X-RAY DIFFRACTION	137	92
2.585-2.592	0.261	447	X-RAY DIFFRACTION	137	92
2.592-2.599	0.252	538	X-RAY DIFFRACTION	137	94
2.599-2.606	0.264	513	X-RAY DIFFRACTION	137	92
2.606-2.614	0.241	531	X-RAY DIFFRACTION	137	93
2.614-2.621	0.25	504	X-RAY DIFFRACTION	137	92
2.621-2.629	0.246	518	X-RAY DIFFRACTION	137	93
2.629-2.637	0.242	534	X-RAY DIFFRACTION	137	91
2.637-2.644	0.241	450	X-RAY DIFFRACTION	137	92
2.644-2.652	0.244	500	X-RAY DIFFRACTION	137	92
2.652-2.66	0.251	621	X-RAY DIFFRACTION	137	92
2.66-2.668	0.261	390	X-RAY DIFFRACTION	137	92
2.668-2.676	0.218	503	X-RAY DIFFRACTION	137	90
2.676-2.685	0.216	551	X-RAY DIFFRACTION	137	94
2.685-2.693	0.228	543	X-RAY DIFFRACTION	137	93
2.693-2.701	0.238	500	X-RAY DIFFRACTION	137	93
2.701-2.71	0.236	457	X-RAY DIFFRACTION	137	92
2.71-2.719	0.23	506	X-RAY DIFFRACTION	137	91
2.719-2.727	0.237	500	X-RAY DIFFRACTION	137	91
2.727-2.736	0.211	480	X-RAY DIFFRACTION	137	90
2.736-2.745	0.221	614	X-RAY DIFFRACTION	137	92
2.745-2.754	0.229	475	X-RAY DIFFRACTION	137	94
2.754-2.764	0.235	475	X-RAY DIFFRACTION	137	92
2.764-2.773	0.197	516	X-RAY DIFFRACTION	137	92
2.773-2.783	0.217	537	X-RAY DIFFRACTION	137	94
2.783-2.792	0.191	438	X-RAY DIFFRACTION	137	90
2.792-2.802	0.228	538	X-RAY DIFFRACTION	137	92
2.802-2.812	0.213	505	X-RAY DIFFRACTION	137	91
2.812-2.822	0.202	527	X-RAY DIFFRACTION	137	91
2.822-2.832	0.178	526	X-RAY DIFFRACTION	137	90
2.832-2.842	0.204	470	X-RAY DIFFRACTION	137	94
2.842-2.853	0.188	463	X-RAY DIFFRACTION	137	89
2.853-2.863	0.204	526	X-RAY DIFFRACTION	137	93
2.863-2.874	0.202	494	X-RAY DIFFRACTION	137	94
2.874-2.885	0.211	553	X-RAY DIFFRACTION	137	94
2.885-2.896	0.219	550	X-RAY DIFFRACTION	137	93
2.896-2.908	0.174	504	X-RAY DIFFRACTION	137	93
2.908-2.919	0.183	480	X-RAY DIFFRACTION	137	91
2.919-2.931	0.192	517	X-RAY DIFFRACTION	137	93
2.931-2.943	0.188	488	X-RAY DIFFRACTION	137	89
2.943-2.955	0.168	517	X-RAY DIFFRACTION	137	90
2.955-2.967	0.2	519	X-RAY DIFFRACTION	137	91
2.967-2.98	0.187	470	X-RAY DIFFRACTION	137	94
2.98-2.992	0.205	587	X-RAY DIFFRACTION	137	92
2.992-3.005	0.181	450	X-RAY DIFFRACTION	137	90
3.005-3.018	0.194	477	X-RAY DIFFRACTION	137	95
3.018-3.032	0.178	512	X-RAY DIFFRACTION	137	90
3.032-3.045	0.19	531	X-RAY DIFFRACTION	137	93
3.045-3.059	0.196	517	X-RAY DIFFRACTION	137	93
3.059-3.073	0.176	508	X-RAY DIFFRACTION	137	91
3.073-3.087	0.183	576	X-RAY DIFFRACTION	137	91
3.087-3.102	0.179	410	X-RAY DIFFRACTION	137	91
3.102-3.117	0.19	568	X-RAY DIFFRACTION	137	93
3.117-3.132	0.182	446	X-RAY DIFFRACTION	137	90
3.132-3.148	0.176	499	X-RAY DIFFRACTION	137	92
3.148-3.163	0.175	526	X-RAY DIFFRACTION	137	94
3.163-3.18	0.186	579	X-RAY DIFFRACTION	137	92
3.18-3.196	0.17	500	X-RAY DIFFRACTION	137	90
3.196-3.213	0.184	439	X-RAY DIFFRACTION	137	93
3.213-3.23	0.189	529	X-RAY DIFFRACTION	137	92
3.23-3.248	0.178	502	X-RAY DIFFRACTION	137	93
3.248-3.266	0.169	549	X-RAY DIFFRACTION	137	94
3.266-3.284	0.158	542	X-RAY DIFFRACTION	137	94
3.284-3.303	0.173	478	X-RAY DIFFRACTION	137	92
3.303-3.322	0.191	491	X-RAY DIFFRACTION	137	92
3.322-3.342	0.177	482	X-RAY DIFFRACTION	137	92
3.342-3.362	0.172	540	X-RAY DIFFRACTION	137	92
3.362-3.382	0.185	513	X-RAY DIFFRACTION	137	91
3.382-3.403	0.186	475	X-RAY DIFFRACTION	137	92
3.403-3.425	0.171	504	X-RAY DIFFRACTION	137	95
3.425-3.447	0.19	526	X-RAY DIFFRACTION	137	92
3.447-3.47	0.191	534	X-RAY DIFFRACTION	137	93
3.47-3.493	0.175	540	X-RAY DIFFRACTION	137	91
3.493-3.518	0.164	457	X-RAY DIFFRACTION	137	89
3.518-3.542	0.181	515	X-RAY DIFFRACTION	137	90
3.542-3.568	0.175	482	X-RAY DIFFRACTION	137	91
3.568-3.594	0.174	542	X-RAY DIFFRACTION	137	94
3.594-3.621	0.157	521	X-RAY DIFFRACTION	137	93
3.621-3.649	0.158	432	X-RAY DIFFRACTION	137	92
3.649-3.678	0.18	568	X-RAY DIFFRACTION	137	92
3.678-3.707	0.156	489	X-RAY DIFFRACTION	137	90
3.707-3.738	0.172	509	X-RAY DIFFRACTION	137	92
3.738-3.77	0.164	511	X-RAY DIFFRACTION	137	94
3.77-3.802	0.157	499	X-RAY DIFFRACTION	137	92
3.802-3.836	0.156	518	X-RAY DIFFRACTION	137	94
3.836-3.872	0.165	496	X-RAY DIFFRACTION	137	89
3.872-3.908	0.151	496	X-RAY DIFFRACTION	137	91
3.908-3.946	0.143	558	X-RAY DIFFRACTION	137	94
3.946-3.985	0.163	438	X-RAY DIFFRACTION	137	89
3.985-4.026	0.137	545	X-RAY DIFFRACTION	137	91
4.026-4.069	0.144	470	X-RAY DIFFRACTION	137	91
4.069-4.114	0.132	524	X-RAY DIFFRACTION	137	91
4.114-4.161	0.124	544	X-RAY DIFFRACTION	137	94
4.161-4.209	0.127	486	X-RAY DIFFRACTION	137	92
4.209-4.261	0.131	482	X-RAY DIFFRACTION	137	93
4.261-4.315	0.128	530	X-RAY DIFFRACTION	137	90
4.315-4.372	0.115	525	X-RAY DIFFRACTION	137	91
4.372-4.431	0.121	447	X-RAY DIFFRACTION	137	90
4.431-4.495	0.117	532	X-RAY DIFFRACTION	137	90
4.495-4.562	0.124	519	X-RAY DIFFRACTION	137	92
4.562-4.633	0.109	470	X-RAY DIFFRACTION	137	89
4.633-4.709	0.13	490	X-RAY DIFFRACTION	137	89
4.709-4.79	0.119	513	X-RAY DIFFRACTION	137	92
4.79-4.877	0.124	482	X-RAY DIFFRACTION	137	91
4.877-4.971	0.123	514	X-RAY DIFFRACTION	137	89
4.971-5.072	0.132	515	X-RAY DIFFRACTION	137	91
5.072-5.182	0.133	475	X-RAY DIFFRACTION	137	90
5.182-5.302	0.137	517	X-RAY DIFFRACTION	137	93
5.302-5.435	0.15	506	X-RAY DIFFRACTION	137	92
5.435-5.582	0.159	511	X-RAY DIFFRACTION	137	90
5.582-5.746	0.157	466	X-RAY DIFFRACTION	137	91
5.746-5.931	0.159	511	X-RAY DIFFRACTION	137	87
5.931-6.142	0.176	483	X-RAY DIFFRACTION	137	87
6.142-6.388	0.163	464	X-RAY DIFFRACTION	137	88
6.388-6.678	0.172	450	X-RAY DIFFRACTION	137	79
6.678-7.029	0.173	449	X-RAY DIFFRACTION	137	81
7.029-7.468	0.154	523	X-RAY DIFFRACTION	137	94
7.468-8.042	0.151	491	X-RAY DIFFRACTION	137	91
8.042-8.847	0.158	469	X-RAY DIFFRACTION	137	85
8.847-10.117	0.159	408	X-RAY DIFFRACTION	137	74
10.117-12.709	0.187	325	X-RAY DIFFRACTION	137	59
12.709-48.736	0.291	281	X-RAY DIFFRACTION	137	50

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	1.3115	0.1496	0.224	1.5077	0.1354	2.8666	0.2524	0.0581	-0.5822	0.3049	-0.0961	-0.2574	0.6474	0.124	-0.1515	0.3749	-0.0163	-0.1239	0.2108	0.0601	0.5929	46.9601	-17.2911	-0.505
2	2.5213	-0.5501	-0.3321	1.3274	0.28	1.0365	0.0568	0.0801	0.1997	0.0196	0.0315	-0.3054	-0.0459	0.042	-0.0915	0.2758	-0.0089	-0.0076	0.363	-0.0408	0.3137	21.7809	3.3575	-20.2161

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A	A	8 - 325
2	X-RAY DIFFRACTION	2	chain B	B	5 - 259

-
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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-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

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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