PDB-3ea5: Kap95p Binding Induces the Switch Loops of RanGDP to adopt the GT...

ID or keywords:

Entry

Database: PDB / ID: 3ea5

Title

Kap95p Binding Induces the Switch Loops of RanGDP to adopt the GTP-bound Conformation: Implications for Nuclear Import Complex Assembly Dynamics

Components

GTP-binding nuclear protein Ran
Importin subunit beta-1

Keywords

TRANSPORT PROTEIN / Karyopherin / Importin / Ran / GTP-binding / Host-virus interaction / Nucleotide-binding / Nucleus / Phosphoprotein / Protein transport / Transport

Function / homology

Function and homology information

Initiation of Nuclear Envelope (NE) Reformation / regulation of protein desumoylation / regulation of nucleocytoplasmic transport / nuclear pore complex assembly / phosphatidylcholine biosynthetic process / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / import into nucleus / cellular response to mineralocorticoid stimulus ...Initiation of Nuclear Envelope (NE) Reformation / regulation of protein desumoylation / regulation of nucleocytoplasmic transport / nuclear pore complex assembly / phosphatidylcholine biosynthetic process / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / import into nucleus / cellular response to mineralocorticoid stimulus / manchette / NLS-dependent protein nuclear import complex / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / protein localization to nucleolus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / GTP metabolic process / NLS-bearing protein import into nucleus / nuclear import signal receptor activity / protein targeting to membrane / nuclear localization sequence binding / MicroRNA (miRNA) biogenesis / spermatid development / DNA metabolic process / male germ cell nucleus / dynein intermediate chain binding / mitotic sister chromatid segregation / viral process / nuclear pore / ribosomal large subunit export from nucleus / mRNA transport / protein export from nucleus / ribosomal subunit export from nucleus / sperm flagellum / Neutrophil degranulation / ribosomal small subunit export from nucleus / centriole / guanyl-nucleotide exchange factor activity / protein import into nucleus / hippocampus development / mitotic spindle organization / positive regulation of protein import into nucleus / Transcriptional regulation by small RNAs / recycling endosome / small GTPase binding / disordered domain specific binding / melanosome / GDP binding / nuclear envelope / mitotic cell cycle / midbody / G protein activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / chromatin binding / GTPase activity / nucleolus / GTP binding / protein-containing complex binding / chromatin / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Forwood, J.K. / Lonhienne, J.K. / Guncar, G. / Stewart, M. / Marfori, M. / Kobe, B.

Citation

Journal: J.Mol.Biol. / Year: 2008
Title: Kap95p binding induces the switch loops of RanGDP to adopt the GTP-bound conformation: implications for nuclear import complex assembly dynamics.
Authors: Forwood, J.K. / Lonhienne, T.G. / Marfori, M. / Robin, G. / Meng, W. / Guncar, G. / Liu, S.M. / Stewart, M. / Carroll, B.J. / Kobe, B.

History

Deposition	Aug 24, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 21, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Oct 20, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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	Feb 21, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3ea5.cif.gz	417.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3ea5.ent.gz	336 KB	Display	PDB format
PDBx/mmJSON format	3ea5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ea/3ea5 ftp://data.pdbj.org/pub/pdb/validation_reports/ea/3ea5	HTTPS FTP

-
Related structure data

Similar structure data	2bku-1 6mq0-d 5syi-d 5il9-d 5sw5-d 5kqq-d 5kqi-d 6cdq-d 5kq0-d 5sxt-d 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	#85 - Jan 2007 Importins similarity (20) #205 - Jan 2017 Nuclear Pore Complex similarity (15) #260 - Aug 2021 Ribonuclease P similarity (1) #88 - Apr 2007 Clathrin similarity (2) #165 - Sep 2013 Designed Protein Cages similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (2) #99 - Mar 2008 Cadherin similarity (2) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #166 - Oct 2013 Proteasome similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #219 - Mar 2018 Vacuolar ATPase similarity (1) #108 - Dec 2008 Hsp90 similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#85 - Jan 2007
Importins
similarity (20)
#205 - Jan 2017
Nuclear Pore Complex
similarity (15)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#88 - Apr 2007
Clathrin
similarity (2)
#165 - Sep 2013
Designed Protein Cages
similarity (1)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (2)
#99 - Mar 2008
Cadherin
similarity (2)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#166 - Oct 2013
Proteasome
similarity (1)
#196 - Apr 2016
Lead Poisoning
similarity (1)
#219 - Mar 2018
Vacuolar ATPase
similarity (1)
#108 - Dec 2008
Hsp90
similarity (1)
#203 - Nov 2016
Aminopeptidase 1 and Autophagy
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#24 - Dec 2001
Glycogen Phosphorylase
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: GTP-binding nuclear protein Ran

B: Importin subunit beta-1

C: GTP-binding nuclear protein Ran

D: Importin subunit beta-1

hetero molecules

240 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GTP-binding nuclear protein Ran

B: Importin subunit beta-1

hetero molecules

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

2

C: GTP-binding nuclear protein Ran

D: Importin subunit beta-1

hetero molecules

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

Unit cell

Length a, b, c (Å)	110.850, 127.810, 171.790
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID	End label comp-ID
1	1	VAL	5	A	A	9 - 224	9 - 224
2	1	VAL	5	C	C	9 - 224	9 - 224
1	2	MET	1	B	B	1 - 32	1 - 32	LEU
2	2	MET	1	D	D	1 - 32	1 - 32	LEU
1	3	SER	1	B	B	33 - 75	33 - 75	VAL
2	3	SER	1	D	D	33 - 75	33 - 75	VAL
1	4	TRP	1	B	B	84 - 106	84 - 106	SER
2	4	TRP	1	D	D	84 - 106	84 - 106	SER
1	5	HIS	1	B	B	129 - 164	129 - 164	GLU
2	5	HIS	1	D	D	129 - 164	129 - 164	GLU
1	6	SER	1	B	B	177 - 188	177 - 188	ALA
2	6		1	D	D	177 - 188	177 - 188	ALA
1	7	PHE	1	B	B	211 - 250	211 - 250	LYS
2	7	PHE	1	D	D	211 - 250	211 - 250	LYS
1	8	ILE	1	B	B	251 - 264	251 - 264	GLU
2	8	ILE	1	D	D	251 - 264	251 - 264	GLU
1	9	GLN	1	B	B	313 - 360	313 - 360	GLN
2	9	GLN	1	D	D	313 - 360	313 - 360	GLN
1	10	ASN	1	B	B	361 - 371	361 - 371	LEU
2	10	ASN	1	D	D	361 - 371	361 - 371	LEU
1	11	ILE	1	B	B	396 - 445	396 - 445	SER
2	11	ILE	1	D	D	396 - 445	396 - 445	SER
1	12	ILE	1	B	B	446 - 474	446 - 474	SER
2	12	ILE	1	D	D	446 - 474	446 - 474	SER
1	13	PRO	1	B	B	491 - 533	491 - 533	ASP
2	13	PRO	1	D	D	491 - 533	491 - 533	ASP
1	14	THR	2	B	B	534 - 556	534 - 556	VAL
2	14	THR	2	D	D	534 - 556	534 - 556	VAL
1	15	GLN	1	B	B	567 - 588	567 - 588	PRO
2	15	GLN	1	D	D	567 - 588	567 - 588	PRO
1	16	VAL	1	B	B	591 - 630	591 - 630	GLY
2	16	VAL	1	D	D	591 - 630	591 - 630	GLY
1	17	LYS	1	B	B	631 - 669	631 - 669	SER
2	17	LYS	1	D	D	631 - 669	631 - 669	SER
1	18	GLU	4	B	B	672 - 712	672 - 712	ASN
2	18	GLU	4	D	D	672 - 712	672 - 712	ASN
1	19	ILE	1	B	B	713 - 741	713 - 741	LEU
2	19	ILE	1	D	D	713 - 741	713 - 741	LEU
1	20	LYS	1	B	B	768 - 820	768 - 820	GLN
2	20	LYS	1	D	D	768 - 820	768 - 820	GLN
1	21	PHE	4	B	B	821 - 861	821 - 861	LEU
2	21	PHE	4	D	D	821 - 861	821 - 861	LEU
1	22	THR	1	B	B	77 - 83	77 - 83	ARG
2	22	THR	1	D	D	77 - 83	77 - 83	ARG
1	23	GLU	1	B	B	108 - 128	108 - 128	PRO
2	23	GLU	1	D	D	108 - 128	108 - 128	PRO
1	24	SER	1	B	B	194 - 210	194 - 210	ILE
2	24	SER	1	D	D	194 - 210	194 - 210	ILE
1	25	ALA	1	B	B	266 - 308	266 - 308	PRO
2	25	ALA	1	D	D	266 - 308	266 - 308	PRO
1	26	SER	1	B	B	310 - 312	310 - 312	LEU
2	26	SER	1	D	D	310 - 312	310 - 312	LEU
1	27	PHE	1	B	B	373 - 395	373 - 395	SER
2	27	PHE	1	D	D	373 - 395	373 - 395	SER
1	28	THR	1	B	B	476 - 490	476 - 490	SER
2	28	THR	1	D	D	476 - 490	476 - 490	SER
1	29	GLU	6	B	B	558 - 566	558 - 566	ALA
2	29	GLU	6	D	D	558 - 566	558 - 566	ALA
1	30	LEU	2	B	B	741 - 745	741 - 745	ASP
2	30	LEU	2	D	D	741 - 745	741 - 745	ASP
1	31	TYR	5	B	B	746 - 767	746 - 767	ASP
2	31	TYR	5	D	D	746 - 767	746 - 767	ASP
1	32	SER	1	B	B	165 - 176	165 - 176	SER
2	32	SER	1	D	D	165 - 176	165 - 176

NCS ensembles :

#1: Protein	GTP-binding nuclear protein Ran / GTPase Ran / Ras-related nuclear protein / Ras-like protein TC4 / Androgen receptor-associated protein 24 Mass: 24488.170 Da / Num. of mol.: 2 / Mutation: A181C, L254K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P62826
#2: Protein	Importin subunit beta-1 / Karyopherin subunit beta-1 / Karyopherin-95 / Importin-95 Mass: 94859.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: KAP95 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q06142
#3: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.55 Å³/Da / Density % sol: 51.75 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 17% PEG 4000 0.1 M MES (pH 6.1) 10 mM MgCl2 125 mM NaCl 12% MPD 5 mg/ml GDP, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 14, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.5→30 Å / Num. obs: 85035 / % possible obs: 99.9 % / Redundancy: 14.6 % / R_merge(I) obs: 0.105 / Net I/σ(I): 12.2
Reflection shell	Resolution: 2.5→2.59 Å / Redundancy: 14.2 % / R_merge(I) obs: 0.585 / Mean I/σ(I) obs: 3.5 / % possible all: 98.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.3.0037	refinement
CrystalClear		data collection
d*TREK		data reduction
d*TREK		data scaling
PHASES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.936 / SU B: 18.977 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.507 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23231	4240	5 %	RANDOM
R_work	0.18942	-	-	-
obs	0.19167	80539	99.98 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 56.138 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	0 Å²	0 Å²
2-	-	-0.09 Å²	0 Å²
3-	-	-	0.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16004	0	60	364	16428

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	16358
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	10797
X-RAY DIFFRACTION	r_angle_refined_deg	1.371	1.963	22219
X-RAY DIFFRACTION	r_angle_other_deg	0.994	3	26518
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.407	5	2045
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.677	25.442	746
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.688	15	2824
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.416	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	2558
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	18187
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3117
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	4018
X-RAY DIFFRACTION	r_nbd_other	0.193	0.2	10593
X-RAY DIFFRACTION	r_nbtor_refined	0.187	0.2	8190
X-RAY DIFFRACTION	r_nbtor_other	0.091	0.2	8453
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.193	0.2	480
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.136	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.461	0.2	10
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.132	0.2	31
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.194	0.2	51
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.218	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	3.659	6	13228
X-RAY DIFFRACTION	r_mcbond_other	0.949	6	4110
X-RAY DIFFRACTION	r_mcangle_it	4.506	10	16530
X-RAY DIFFRACTION	r_scbond_it	3.729	6	7058
X-RAY DIFFRACTION	r_scangle_it	5.175	10	5689

Refine LS restraints NCS

Ens-ID	Dom-ID	Number	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	995	X-RAY DIFFRACTION	MEDIUM POSITIONAL	0.12	0.15
1	1	1410	X-RAY DIFFRACTION	LOOSE POSITIONAL	0.22	0.4
1	1	995	X-RAY DIFFRACTION	MEDIUM THERMAL	3.1	10
1	1	1410	X-RAY DIFFRACTION	LOOSE THERMAL	3.2	15
2	1	423	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.03	0.05
2	1	423	X-RAY DIFFRACTION	TIGHT THERMAL	1.76	7
3	1	545	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.04	0.05
3	1	545	X-RAY DIFFRACTION	TIGHT THERMAL	2.21	7
4	1	288	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.04	0.05
4	1	288	X-RAY DIFFRACTION	TIGHT THERMAL	2.24	7
5	1	467	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.04	0.05
5	1	467	X-RAY DIFFRACTION	TIGHT THERMAL	2.36	7
6	1	110	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.04	0.05
6	1	110	X-RAY DIFFRACTION	TIGHT THERMAL	5.82	7
7	1	528	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.05	0.05
7	1	528	X-RAY DIFFRACTION	TIGHT THERMAL	2.61	7
8	1	222	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.03	0.05
8	1	222	X-RAY DIFFRACTION	TIGHT THERMAL	2.79	7
9	1	618	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.04	0.05
9	1	618	X-RAY DIFFRACTION	TIGHT THERMAL	2.12	7
10	1	135	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.03	0.05
10	1	135	X-RAY DIFFRACTION	TIGHT THERMAL	1.99	7
11	1	650	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.05	0.05
11	1	650	X-RAY DIFFRACTION	TIGHT THERMAL	2.42	7
12	1	352	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.05	0.05
12	1	352	X-RAY DIFFRACTION	TIGHT THERMAL	2.91	7
13	1	542	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.04	0.05
13	1	542	X-RAY DIFFRACTION	TIGHT THERMAL	1.74	7
14	1	137	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.05	0.05
14	1	129	X-RAY DIFFRACTION	MEDIUM POSITIONAL	0.12	0.15
14	1	137	X-RAY DIFFRACTION	TIGHT THERMAL	1.83	7
14	1	129	X-RAY DIFFRACTION	MEDIUM THERMAL	2.4	10
15	1	281	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.05	0.05
15	1	281	X-RAY DIFFRACTION	TIGHT THERMAL	2.33	7
16	1	517	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.06	0.05
16	1	517	X-RAY DIFFRACTION	TIGHT THERMAL	1.81	7
17	1	504	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.05	0.05
17	1	504	X-RAY DIFFRACTION	TIGHT THERMAL	2.06	7
18	1	551	X-RAY DIFFRACTION	MEDIUM POSITIONAL	0.15	0.15
18	1	551	X-RAY DIFFRACTION	MEDIUM THERMAL	2.72	10
19	1	351	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.03	0.05
19	1	351	X-RAY DIFFRACTION	TIGHT THERMAL	2.06	7
20	1	673	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.03	0.05
20	1	673	X-RAY DIFFRACTION	TIGHT THERMAL	1.68	7
21	1	617	X-RAY DIFFRACTION	MEDIUM POSITIONAL	0.21	0.15
21	1	617	X-RAY DIFFRACTION	MEDIUM THERMAL	2.34	10
22	1	106	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.03	0.05
22	1	106	X-RAY DIFFRACTION	TIGHT THERMAL	2.67	7
23	1	248	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.03	0.05
23	1	248	X-RAY DIFFRACTION	TIGHT THERMAL	2.08	7
24	1	197	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.04	0.05
24	1	197	X-RAY DIFFRACTION	TIGHT THERMAL	2.52	7
25	1	557	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.04	0.05
25	1	557	X-RAY DIFFRACTION	TIGHT THERMAL	1.99	7
26	1	37	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.03	0.05
26	1	37	X-RAY DIFFRACTION	TIGHT THERMAL	3.21	7
27	1	307	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.03	0.05
27	1	307	X-RAY DIFFRACTION	TIGHT THERMAL	2.04	7
28	1	177	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.04	0.05
28	1	177	X-RAY DIFFRACTION	TIGHT THERMAL	2.06	7
29	1	112	X-RAY DIFFRACTION	LOOSE POSITIONAL	0.56	0.4
29	1	112	X-RAY DIFFRACTION	LOOSE THERMAL	4.42	15
30	1	30	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.02	0.05
30	1	30	X-RAY DIFFRACTION	MEDIUM POSITIONAL	0.03	0.15
30	1	30	X-RAY DIFFRACTION	TIGHT THERMAL	1.57	7
30	1	30	X-RAY DIFFRACTION	MEDIUM THERMAL	0.98	10
31	1	130	X-RAY DIFFRACTION	MEDIUM POSITIONAL	0.07	0.15
31	1	139	X-RAY DIFFRACTION	LOOSE POSITIONAL	0.22	0.4
31	1	130	X-RAY DIFFRACTION	MEDIUM THERMAL	1.91	10
31	1	139	X-RAY DIFFRACTION	LOOSE THERMAL	3.31	15
32	1	17	X-RAY DIFFRACTION	TIGHT POSITIONAL	0.04	0.05
32	1	17	X-RAY DIFFRACTION	TIGHT THERMAL	6.87	7

LS refinement shell

Resolution: 2.5→2.564 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.325	294	-
R_work	0.25	5872	-
obs	-	119851	99.95 %

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	3.1364	1.1556	0.4211	8.6862	-2.7536	5.9345	0.1656	0.537	0.1438	-0.5568	-0.222	-0.4529	0.1626	0.2913	0.0564	-0.1427	0.0248	0.1166	-0.0057	-0.0258	-0.0478	63.452	-0.363	-13.218
2	4.0796	2.765	1.3874	9.6211	1.9694	7.364	-0.2026	-0.2147	-0.4393	0.1269	-0.23	0.8952	0.3996	-0.9023	0.4325	0.0131	0.0466	0.1588	0.0767	-0.0322	0.2802	-28.777	6.356	35.22
3	4.0712	1.0461	0.203	5.7225	-0.0381	3.315	-0.0509	0.2505	-0.0612	-0.1737	0.1585	-0.148	0.1666	0.1222	-0.1077	-0.2379	-0.0015	0.0192	-0.2283	-0.0165	-0.2192	57.193	-5.296	-2.48
4	2.8624	-0.0119	0.3427	8.2671	1.047	3.2268	-0.1021	-0.0894	-0.1471	0.0435	0.0706	0.1682	-0.0637	-0.0544	0.0314	-0.0821	0.038	-0.0031	-0.076	-0.0292	-0.1298	-16.813	12.4	35.872
5	2.3363	0.0408	0.4684	6.486	1.7053	2.9185	-0.0235	-0.1046	-0.1892	0.0932	0.0305	-0.3025	0.1431	0.1409	-0.0071	-0.2585	0.0263	-0.0008	-0.1983	0.0067	-0.2223	57.932	-5.611	7.03
6	2.4809	-2.4463	0.9633	14.1849	-2.2781	5.9465	-0.1287	-0.1987	-0.0666	0.7432	0.1931	-0.234	0.0917	0.0884	-0.0644	-0.0686	0.0587	-0.0336	-0.048	-0.0295	-0.1445	-9.712	14.285	42.035
7	1.5364	-1.6009	-0.2149	4.1799	2.7622	4.5679	0.1301	-0.1878	-0.2523	0.4591	-0.2561	0.2209	0.3969	-0.1073	0.1261	-0.231	0.0133	-0.031	-0.1403	0.02	-0.1277	54.802	0.237	17.197
8	5.3385	-0.6711	0.8805	8.7768	-0.2662	2.4784	-0.0466	-0.5652	0.6252	0.8313	-0.2524	-0.979	-0.4167	0.6079	0.299	0.2711	0.1237	-0.077	0.2436	-0.0599	0.1477	0.859	10.133	46.055
9	10.7606	0.5272	2.0507	1.6687	1.5951	10.6651	0.1978	0.1227	-0.9978	0.3098	-0.0559	-0.2547	0.8512	-0.5151	-0.142	-0.2285	0.0474	-0.0379	-0.1025	0.009	-0.1777	46.732	5.428	19.705
10	2.4776	1.4889	-1.7382	5.5193	-5.2781	18.233	0.0567	-0.4146	-0.0242	0.7271	0.0347	-0.0876	-0.8214	0.3282	-0.0914	0.1285	0.0929	-0.0176	0.0957	-0.058	0.1414	8.168	1.561	43.152
11	6.5501	0.7985	-0.8282	5.0163	-1.8914	5.9626	-0.0252	-0.092	0.0713	0.1675	-0.0467	-0.1976	-0.0037	-0.0162	0.0719	-0.2595	0.0557	-0.0177	-0.144	-0.0046	-0.2251	40.123	11.433	22.563
12	5.3753	1.0189	0.8914	7.57	-0.0201	3.053	0.1762	-0.1705	0.1091	0.5031	-0.0901	-0.1046	0.0048	-0.1084	-0.086	0.0501	0.0721	-0.0062	0.0586	-0.0752	-0.036	15.076	-0.742	37.715
13	2.336	1.563	-0.3134	6.0465	-1.6937	3.2029	-0.0491	0.002	0.1175	0.0192	0.0302	0.2644	0.0514	-0.0191	0.019	-0.2578	0.0735	-0.0001	-0.1302	0.0168	-0.1817	27.918	16.424	17.911
14	2.6539	1.5414	-1.1618	5.8889	-1.7166	5.5341	-0.1893	-0.0038	-0.0966	0.0562	-0.059	0.1489	0.4662	-0.094	0.2484	-0.0214	0.0336	0.0233	-0.0603	-0.0674	-0.0186	18.459	-7.767	26.182
15	1.7573	0.4952	0.0215	5.845	-0.8472	2.7096	-0.0086	-0.0224	0.0801	-0.0349	0.0496	0.0021	-0.2152	0.0099	-0.0409	-0.2914	0.0254	-0.0395	-0.1693	0.0085	-0.1736	28.681	28.787	10.813
16	3.8545	4.0804	0.5723	7.9181	-1.6338	2.6079	0.306	0.0596	-0.1869	0.4456	-0.0424	0.2266	0.3157	-0.079	-0.2635	0.2015	0.0263	0.0127	-0.0629	-0.0916	-0.0345	13.226	-20.98	25.276
17	6.4145	4.237	-1.8011	8.4083	-1.491	3.3248	0.0843	-0.4247	0.1485	0.2184	-0.0272	0.1389	-0.3786	0.1583	-0.0571	-0.2707	0.0261	-0.0591	-0.175	-0.0083	-0.2695	22.075	38.474	9.553
18	2.5974	2.6748	-1.8707	9.2522	-2.444	3.628	0.1177	-0.2545	-0.3048	0.5469	-0.178	-0.6436	0.2541	0.4701	0.0602	0.1961	0.0502	-0.1069	-0.0428	-0.035	-0.0253	16.297	-31.46	20.927
19	5.0116	-0.1669	-2.3433	2.0449	-1.1352	4.4446	0.0517	0.1831	-0.2154	-0.2077	-0.0599	-0.0039	-0.241	-0.172	0.0083	-0.2251	0.0241	-0.0593	-0.2187	-0.0386	-0.2242	16.642	37.127	0.384
20	6.9628	2.2874	-1.1978	4.5251	0.1884	4.0343	0.0141	0.4333	0.0252	0.1625	0.1214	-0.1646	-0.1351	0.1788	-0.1354	0.0588	0.0336	-0.0456	-0.1223	-0.0518	-0.0436	12.112	-32.098	11.041
21	10.8246	-0.0977	0.3511	4.537	0.2237	4.6498	-0.1894	0.1476	-0.0737	-0.1318	0.1733	0.2051	-0.1221	-0.4684	0.016	-0.115	0.0527	-0.0216	-0.1635	-0.0357	-0.3022	17.077	37.285	-11.564
22	3.806	-1.2939	-0.807	6.1467	1.2054	5.3776	-0.0477	0.2418	0.2715	0.087	0.1748	-0.1581	-0.3621	0.1907	-0.127	-0.1126	-0.0285	-0.0398	-0.1839	-0.0358	-0.0694	2.512	-33.546	4.351
23	7.101	-1.54	-0.7839	3.9814	-0.0098	2.8403	-0.0651	0.2013	0.2616	-0.175	-0.0528	0.1635	-0.3289	-0.2674	0.1179	-0.1259	0.0012	-0.0718	-0.1903	-0.0425	-0.2828	20.324	35.357	-20.325
24	4.6989	-1.2857	-1.5616	5.4054	1.2517	1.883	0.0301	0.1147	-0.1067	0.0298	-0.0433	0.0666	-0.0045	-0.1049	0.0131	-0.099	-0.0045	-0.0403	-0.175	0.0028	-0.1184	-6.261	-32.058	0.977
25	7.1086	-0.5234	-1.0328	3.394	0.0026	4.3206	-0.11	0.1902	0.0576	-0.2747	-0.0265	0.0217	-0.0592	-0.1306	0.1364	-0.0739	-0.0124	-0.0408	-0.2223	-0.0346	-0.2647	27.687	30.313	-30.345
26	5.5109	-0.5782	-2.5062	5.3488	1.0118	7.579	0.0347	0.3453	-0.185	0.1231	-0.0829	0.5316	0.3693	-0.4562	0.0481	-0.0891	-0.0262	-0.0616	-0.1497	-0.0353	0.0185	-18.622	-27.579	-0.042
27	10.6723	1.0353	4.8027	5.3026	-0.4689	8.0718	-0.2374	0.1893	0.567	-0.4501	0.0177	0.1896	-0.4666	-0.0263	0.2198	-0.041	-0.0174	-0.0609	-0.1462	-0.0761	-0.2427	24.895	22.096	-37.455
28	6.5359	1.7664	4.0039	8.2517	0.5674	9.8855	0.183	0.4016	-0.2087	-0.5889	-0.1899	0.1342	0.5565	-0.3779	0.0068	-0.0814	0.0306	-0.0356	-0.0429	-0.0131	-0.0063	-23.097	-19.789	-7.214
29	4.9059	0.597	0.9977	8.2991	-1.0174	4.1387	-0.1634	-0.0664	-0.1241	-0.1657	0.0021	-0.0417	0.0338	0.1217	0.1614	-0.069	-0.0576	0.0052	-0.0512	-0.0609	-0.2179	20.9	11.333	-40.768
30	5.0101	2.5425	-2.0798	13.101	-4.6934	2.3825	-0.0382	0.1692	0.213	0.0746	0.4246	1.3181	0.2997	-0.9486	-0.3863	-0.059	0.011	0.0321	0.1151	0.0776	0.1978	-23.924	-8.999	-12.197
31	8.2379	1.2482	1.5267	6.0436	-0.456	11.4467	-0.1046	0.1337	-0.2296	-0.0928	-0.0678	-0.5433	0.0456	0.8281	0.1725	-0.1301	-0.0029	0.0533	-0.1426	-0.069	-0.0883	16.973	0.936	-41.028
32	5.7544	-0.8606	-0.0953	4.7341	0.6926	11.1853	0.1565	0.0514	0.0395	0.0497	0.0254	0.3976	0.0859	-0.7956	-0.1819	-0.0557	0.0735	0.072	-0.0247	0.024	0.0254	-22.097	1.527	-15.045
33	4.4695	0.3954	-0.9653	4.3903	-1.3047	6.7757	-0.1138	-0.3976	-0.3755	0.3467	-0.2141	-0.4003	0.3567	0.3401	0.3278	-0.1881	-0.0066	0.0502	-0.139	0.0031	-0.1065	10.643	-7.689	-36.448
34	5.6472	0.701	-0.1724	5.0635	0.3673	6.1535	0.1522	-0.3494	0.2936	0.0923	0.0738	0.1022	-0.5764	-0.0219	-0.226	0.0746	0.0929	0.1637	-0.0979	0.0215	-0.0392	-14.892	9.905	-18.697
35	4.418	-0.6969	-2.3654	3.8127	1.4271	10.4248	-0.0844	0.0786	-0.5705	0.0406	-0.0573	0.0404	0.6146	-0.3585	0.1417	-0.1729	-0.0607	0.0914	-0.1441	-0.0376	-0.0828	-1.071	-11.584	-37.094
36	6.6008	-2.0834	-2.1898	5.604	-1.2667	3.7241	0.3734	0.214	0.581	-0.0784	0.0801	0.2243	-0.9469	-0.5241	-0.4534	0.1872	0.0886	0.1823	-0.035	0.0123	-0.0455	-10.658	14.246	-29.635
37	5.9172	-0.2062	-1.8885	9.6103	4.4873	5.3662	-0.2513	0.0904	-0.7658	0.2466	-0.1986	0.9045	0.8449	-0.8826	0.4498	-0.0417	-0.0834	0.1186	0.0448	-0.0824	0.1551	-11.027	-11.406	-31.787
38	3.3568	-4.7317	-1.9221	11.7547	-0.6542	3.3256	0.5298	0.7074	0.8495	-0.2911	-0.2929	-0.006	-1.0109	0.0249	-0.2369	0.263	0.0368	0.2177	0.0475	0.0401	0.0644	-1.809	13.992	-36.772
39	3.3815	-0.2042	0.7015	3.186	-0.3019	2.1379	0.0164	-0.0337	0.1235	-0.0523	0.0218	0.0531	-0.0931	-0.0741	-0.0381	-0.2885	-0.0354	0.0167	-0.2512	-0.0261	-0.2801	43.327	16.885	-11.283
40	2.4267	-0.223	-0.2183	4.6139	1.043	4.4487	-0.1248	-0.1577	-0.2237	0.3028	0.102	-0.0379	0.3286	0.1406	0.0227	-0.0208	0.0255	0.0495	-0.1429	0.0006	-0.0733	-13.74	-11.346	22.625

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	1 - 32
2	X-RAY DIFFRACTION	2	D	1 - 32
3	X-RAY DIFFRACTION	3	B	33 - 83
4	X-RAY DIFFRACTION	4	D	33 - 83
5	X-RAY DIFFRACTION	5	B	84 - 128
6	X-RAY DIFFRACTION	6	D	84 - 128
7	X-RAY DIFFRACTION	7	B	129 - 164
8	X-RAY DIFFRACTION	8	D	129 - 164
9	X-RAY DIFFRACTION	9	B	165 - 210
10	X-RAY DIFFRACTION	10	D	165 - 210
11	X-RAY DIFFRACTION	11	B	211 - 250
12	X-RAY DIFFRACTION	12	D	211 - 250
13	X-RAY DIFFRACTION	13	B	251 - 312
14	X-RAY DIFFRACTION	14	D	251 - 312
15	X-RAY DIFFRACTION	15	B	313 - 360
16	X-RAY DIFFRACTION	16	D	313 - 360
17	X-RAY DIFFRACTION	17	B	361 - 395
18	X-RAY DIFFRACTION	18	D	361 - 395
19	X-RAY DIFFRACTION	19	B	396 - 445
20	X-RAY DIFFRACTION	20	D	396 - 445
21	X-RAY DIFFRACTION	21	B	450 - 490
22	X-RAY DIFFRACTION	22	D	450 - 490
23	X-RAY DIFFRACTION	23	B	491 - 533
24	X-RAY DIFFRACTION	24	D	491 - 533
25	X-RAY DIFFRACTION	25	B	534 - 588
26	X-RAY DIFFRACTION	26	D	534 - 588
27	X-RAY DIFFRACTION	27	B	589 - 630
28	X-RAY DIFFRACTION	28	D	589 - 630
29	X-RAY DIFFRACTION	29	B	631 - 670
30	X-RAY DIFFRACTION	30	D	631 - 670
31	X-RAY DIFFRACTION	31	B	671 - 712
32	X-RAY DIFFRACTION	32	D	671 - 712
33	X-RAY DIFFRACTION	33	B	713 - 768
34	X-RAY DIFFRACTION	34	D	713 - 768
35	X-RAY DIFFRACTION	35	B	769 - 820
36	X-RAY DIFFRACTION	36	D	769 - 820
37	X-RAY DIFFRACTION	37	B	821 - 861
38	X-RAY DIFFRACTION	38	D	821 - 861
39	X-RAY DIFFRACTION	39	A	9 - 179
40	X-RAY DIFFRACTION	40	C	9 - 177

-
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

-
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

-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

-
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