PDB-3exg: Crystal structure of the pyruvate dehydrogenase (E1p) component o...

ID or keywords:

Entry

Database: PDB / ID: 3exg

Title

Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex

Components

Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial
Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

Keywords

OXIDOREDUCTASE /

heterotetramer / thiamine diphosphate-dependent enzyme / Disease mutation /

Glycolysis / Leigh syndrome /

Mitochondrion /

Phosphoprotein /

Alternative splicing / Polymorphism /

Pyruvate /

Thiamine pyrophosphate / Transit peptide

Function / homology

Function and homology information

pyruvate dehydrogenase (NAD+) activity /

pyruvate dehydrogenase (acetyl-transferring) /

pyruvate dehydrogenase (acetyl-transferring) activity / acetyl-CoA biosynthetic process from pyruvate /

pyruvate dehydrogenase complex /

: /

Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.011 Å

Authors

Kato, M. / Wynn, R.M. / Chuang, J.L. / Tso, S.-C. / Machius, M. / Li, J. / Chuang, D.T.

Citation

Journal: Structure / Year: 2008
Title: Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops.
Authors: Kato, M. / Wynn, R.M. / Chuang, J.L. / Tso, S.C. / Machius, M. / Li, J. / Chuang, D.T.

History

Deposition	Oct 16, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 25, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Oct 20, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4	Dec 27, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3exg.cif.gz	1.9 MB	Display	PDBx/mmCIF format
PDB format	pdb3exg.ent.gz	1.6 MB	Display	PDB format
PDBx/mmJSON format	3exg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	3exeC 3exfC 3exhC 3exiC C: citing same article (ref.)
Similar structure data	6cer-1 1olu-1 6q6q-d 4uhw-d 2ozl-d 3exe-1 4uhx-d 1fiq-d 5epg-d 2bfb-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) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (10) #154 - Oct 2012 Citric Acid Cycle similarity (6) #155 - Nov 2012 Vitamin D Receptor similarity (2) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

B: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

C: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

D: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

E: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

F: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

G: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

H: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

I: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

J: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

K: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

L: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

M: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

N: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

O: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

P: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

Q: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

R: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

S: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

T: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

U: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

V: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

W: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

X: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

Y: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

Z: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

1: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

2: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

3: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

4: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

5: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

6: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

hetero molecules

1.26 MDa, 32 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

B: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

C: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

D: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

hetero molecules

defined by author&software
157 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

F: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

G: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

H: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

hetero molecules

defined by author&software
157 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

I: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

J: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

K: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

L: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

hetero molecules

defined by author&software
157 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

M: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

N: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

O: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

P: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

hetero molecules

defined by author&software
157 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

Q: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

R: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

S: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

T: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

hetero molecules

defined by author&software
157 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

U: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

V: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

W: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

X: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

hetero molecules

defined by author&software
157 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

Y: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

Z: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

1: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

2: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

hetero molecules

defined by author&software
157 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

3: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

4: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

5: Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

6: Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

hetero molecules

defined by author&software
157 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	119.278, 128.290, 228.410
Angle α, β, γ (deg.)	90.140, 90.050, 90.020
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 5

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	A	A	0 - 196	0 - 196
2	1	1	C	C	0 - 196	0 - 196
3	1	1	E	E	0 - 196	0 - 196
4	1	1	G	G	0 - 196	0 - 196
5	1	1	I	I	0 - 196	0 - 196
6	1	1	K	K	0 - 196	0 - 196
7	1	1	M	M	0 - 196	0 - 196
8	1	1	O	O	0 - 196	0 - 196
9	1	1	Q	Q	0 - 196	0 - 196
10	1	1	S	S	0 - 196	0 - 196
11	1	1	U	U	0 - 196	0 - 196
12	1	1	W	W	0 - 196	0 - 196
13	1	1	Y	Y	0 - 196	0 - 196
14	1	1	A	A	0 - 196	0 - 196
15	1	1	C	C	0 - 196	0 - 196
16	1	1	E	E	0 - 196	0 - 196
1	2	1	A	A	207 - 260	207 - 260
2	2	1	C	C	207 - 260	207 - 260
3	2	1	E	E	207 - 260	207 - 260
4	2	1	G	G	207 - 260	207 - 260
5	2	1	I	I	207 - 260	207 - 260
6	2	1	K	K	207 - 260	207 - 260
7	2	1	M	M	207 - 260	207 - 260
8	2	1	O	O	207 - 260	207 - 260
9	2	1	Q	Q	207 - 260	207 - 260
10	2	1	S	S	207 - 260	207 - 260
11	2	1	U	U	207 - 260	207 - 260
12	2	1	W	W	207 - 260	207 - 260
13	2	1	Y	Y	207 - 260	207 - 260
14	2	1	A	A	207 - 260	207 - 260
15	2	1	C	C	207 - 260	207 - 260
16	2	1	E	E	207 - 260	207 - 260
1	3	1	A	A	280 - 361	280 - 361
2	3	1	C	C	280 - 361	280 - 361
3	3	1	E	E	280 - 361	280 - 361
4	3	1	G	G	280 - 361	280 - 361
5	3	1	I	I	280 - 361	280 - 361
6	3	1	K	K	280 - 361	280 - 361
7	3	1	M	M	280 - 361	280 - 361
8	3	1	O	O	280 - 361	280 - 361
9	3	1	Q	Q	280 - 361	280 - 361
10	3	1	S	S	280 - 361	280 - 361
11	3	1	U	U	280 - 361	280 - 361
12	3	1	W	W	280 - 361	280 - 361
13	3	1	Y	Y	280 - 361	280 - 361
14	3	1	A	A	280 - 361	280 - 361
15	3	1	C	C	280 - 361	280 - 361
16	3	1	E	E	280 - 361	280 - 361
1	1	2	B	B	1 - 329	1 - 329
2	1	2	D	D	1 - 329	1 - 329
3	1	2	F	F	1 - 329	1 - 329
4	1	2	H	H	1 - 329	1 - 329
5	1	2	J	J	1 - 329	1 - 329
6	1	2	L	L	1 - 329	1 - 329
7	1	2	N	N	1 - 329	1 - 329
8	1	2	P	P	1 - 329	1 - 329
9	1	2	R	R	1 - 329	1 - 329
10	1	2	T	T	1 - 329	1 - 329
11	1	2	V	V	1 - 329	1 - 329
12	1	2	X	X	1 - 329	1 - 329
13	1	2	Z	Z	1 - 329	1 - 329
14	1	2	B	B	1 - 329	1 - 329
15	1	2	D	D	1 - 329	1 - 329
16	1	2	F	F	1 - 329	1 - 329

NCS ensembles :

ID
1
2

#1: Protein	Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial / E.C.1.2.4.1 / pyruvate dehydrogenase (E1p) alpha subunit / PDHE1-A type I Mass: 42552.516 Da / Num. of mol.: 16 / Fragment: E1p-alpha / Mutation: S203A,S271A Source method: isolated from a genetically manipulated source Details: Phosphorylation site 1 (S264) only mutant (S203A/S271A) with the site 1 being phosphorylated. Apo form Source: (gene. exp.) Homo sapiens (human) / Gene: PDHA1, PHE1A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P08559, pyruvate dehydrogenase (acetyl-transferring)
#2: Protein	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial / E.C.1.2.4.1 / pyruvate dehydrogenase (E1p) beta subunit / PDHE1-B Mass: 35941.316 Da / Num. of mol.: 16 / Fragment: E1p-beta Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDHB, PHE1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P11177, pyruvate dehydrogenase (acetyl-transferring)
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: K

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.78 Å³/Da / Density % sol: 55.8 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEG 8000, 140mM NaOAC, 50mM BisTris pH6.5, 10% glucose, 50mM Taurine, 8mM MgCl2, and 10mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.98 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2008

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 3.011→50 Å / Num. obs: 263005 / % possible obs: 98.4 % / Redundancy: 2.1 % / R_merge(I) obs: 0.08 / Χ²: 1.283 / Net I/σ(I): 10.299

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
3.011-3.05	1.9	0.535	13124	1.687	1	98
3.05-3.11	2	0.464	13107	1.744	1	98.1
3.11-3.17	2	0.38	13091	1.657	1	98.1
3.17-3.23	2	0.307	13121	1.531	1	98.3
3.23-3.3	2	0.262	13157	1.397	1	98.4
3.3-3.38	2	0.227	13150	1.324	1	98.3
3.38-3.46	2	0.185	13125	1.29	1	98.4
3.46-3.56	2	0.157	13196	1.315	1	98.4
3.56-3.66	2	0.13	13089	1.319	1	98.3
3.66-3.78	2	0.109	13143	1.266	1	98.3
3.78-3.91	2.1	0.096	13088	1.302	1	98.3
3.91-4.07	2.1	0.078	13161	1.274	1	98.2
4.07-4.26	2.1	0.064	13135	1.268	1	98.1
4.26-4.48	2.1	0.055	13076	1.276	1	98.1
4.48-4.76	2.1	0.047	13186	1.148	1	98.6
4.76-5.13	2.1	0.046	13221	1.102	1	98.7
5.13-5.64	2.1	0.047	13177	1.118	1	98.9
5.64-6.46	2.1	0.041	13207	1.055	1	99
6.46-8.13	2.2	0.029	13252	0.993	1	99.3
8.13-50	2.1	0.02	13199	0.806	1	98.7

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.4.0069	refinement
PDB_EXTRACT	3.006	data extraction
ADSC	Quantum	data collection
HKL-2000		data reduction

Refinement

Resolution: 3.011→50 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.921 / Occupancy max: 1 / Occupancy min: 1 / SU B: 44.287 / SU ML: 0.35 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.253	13221	5 %	RANDOM
R_work	0.189	-	-	-
obs	0.192	262510	97.91 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 108.47 Å² / B_iso mean: 55.677 Å² / B_iso min: 30.75 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.66 Å²	-0.24 Å²	-0.18 Å²
2-	-	-4.73 Å²	0.49 Å²
3-	-	-	1.07 Å²

Refinement step

Cycle: LAST / Resolution: 3.011→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	83323	0	16	0	83339

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	85013
X-RAY DIFFRACTION	r_angle_refined_deg	1.883	1.964	114852
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.426	5	10701
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.653	24.021	3810
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.199	15	14628
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.113	15	577
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	12492
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	64719
X-RAY DIFFRACTION	r_mcbond_it	0.591	1.5	53377
X-RAY DIFFRACTION	r_mcangle_it	1.203	2	85616
X-RAY DIFFRACTION	r_scbond_it	2	3	31636
X-RAY DIFFRACTION	r_scangle_it	3.488	4.5	29236

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	14	A	1320	MEDIUM POSITIONAL	0.21	0.5
1	1	C	1320	MEDIUM POSITIONAL	0.23	0.5
1	15	E	1320	MEDIUM POSITIONAL	0.2	0.5
1	1	G	1320	MEDIUM POSITIONAL	0.21	0.5
1	16	I	1320	MEDIUM POSITIONAL	0.21	0.5
1	1	K	1320	MEDIUM POSITIONAL	0.22	0.5
1	1	M	1320	MEDIUM POSITIONAL	0.21	0.5
1	1	O	1320	MEDIUM POSITIONAL	0.28	0.5
1	1	Q	1320	MEDIUM POSITIONAL	0.2	0.5
1	1	S	1320	MEDIUM POSITIONAL	0.23	0.5
1	14	U	1320	MEDIUM POSITIONAL	0.2	0.5
1	1	W	1320	MEDIUM POSITIONAL	0.21	0.5
1	15	Y	1320	MEDIUM POSITIONAL	0.21	0.5
1	1	A	1320	MEDIUM POSITIONAL	0.28	0.5
1	16	C	1320	MEDIUM POSITIONAL	0.22	0.5
1	1	E	1320	MEDIUM POSITIONAL	0.22	0.5
1	14	A	1244	LOOSE POSITIONAL	0.47	5
1	1	C	1244	LOOSE POSITIONAL	0.46	5
1	15	E	1244	LOOSE POSITIONAL	0.4	5
1	1	G	1244	LOOSE POSITIONAL	0.43	5
1	16	I	1244	LOOSE POSITIONAL	0.39	5
1	1	K	1244	LOOSE POSITIONAL	0.45	5
1	1	M	1244	LOOSE POSITIONAL	0.39	5
1	1	O	1244	LOOSE POSITIONAL	0.5	5
1	1	Q	1244	LOOSE POSITIONAL	0.48	5
1	1	S	1244	LOOSE POSITIONAL	0.46	5
1	14	U	1244	LOOSE POSITIONAL	0.41	5
1	1	W	1244	LOOSE POSITIONAL	0.49	5
1	15	Y	1244	LOOSE POSITIONAL	0.4	5
1	1	A	1244	LOOSE POSITIONAL	0.54	5
1	16	C	1244	LOOSE POSITIONAL	0.45	5
1	1	E	1244	LOOSE POSITIONAL	0.46	5
1	14	A	1320	MEDIUM THERMAL	2.3	2
1	1	C	1320	MEDIUM THERMAL	2.37	2
1	15	E	1320	MEDIUM THERMAL	2.55	2
1	1	G	1320	MEDIUM THERMAL	2.28	2
1	16	I	1320	MEDIUM THERMAL	2.25	2
1	1	K	1320	MEDIUM THERMAL	2.19	2
1	1	M	1320	MEDIUM THERMAL	2.4	2
1	1	O	1320	MEDIUM THERMAL	2.85	2
1	1	Q	1320	MEDIUM THERMAL	2.26	2
1	1	S	1320	MEDIUM THERMAL	1.98	2
1	14	U	1320	MEDIUM THERMAL	2.7	2
1	1	W	1320	MEDIUM THERMAL	2.01	2
1	15	Y	1320	MEDIUM THERMAL	2.53	2
1	1	A	1320	MEDIUM THERMAL	2.57	2
1	16	C	1320	MEDIUM THERMAL	2.39	2
1	1	E	1320	MEDIUM THERMAL	2.01	2
1	14	A	1244	LOOSE THERMAL	3.13	10
1	1	C	1244	LOOSE THERMAL	3.11	10
1	15	E	1244	LOOSE THERMAL	3.37	10
1	1	G	1244	LOOSE THERMAL	3.12	10
1	16	I	1244	LOOSE THERMAL	2.98	10
1	1	K	1244	LOOSE THERMAL	2.86	10
1	1	M	1244	LOOSE THERMAL	3.2	10
1	1	O	1244	LOOSE THERMAL	3.46	10
1	1	Q	1244	LOOSE THERMAL	3.07	10
1	1	S	1244	LOOSE THERMAL	3.03	10
1	14	U	1244	LOOSE THERMAL	3.35	10
1	1	W	1244	LOOSE THERMAL	2.76	10
1	15	Y	1244	LOOSE THERMAL	3.08	10
1	1	A	1244	LOOSE THERMAL	3.25	10
1	16	C	1244	LOOSE THERMAL	3.13	10
1	1	E	1244	LOOSE THERMAL	2.77	10
2	1	B	1316	MEDIUM POSITIONAL	0.19	0.5
2	14	D	1316	MEDIUM POSITIONAL	0.18	0.5
2	1	F	1316	MEDIUM POSITIONAL	0.18	0.5
2	15	H	1316	MEDIUM POSITIONAL	0.18	0.5
2	1	J	1316	MEDIUM POSITIONAL	0.19	0.5
2	16	L	1316	MEDIUM POSITIONAL	0.18	0.5
2	1	N	1316	MEDIUM POSITIONAL	0.18	0.5
2	1	P	1316	MEDIUM POSITIONAL	0.18	0.5
2	1	R	1316	MEDIUM POSITIONAL	0.18	0.5
2	1	T	1316	MEDIUM POSITIONAL	0.2	0.5
2	1	V	1316	MEDIUM POSITIONAL	0.19	0.5
2	14	X	1316	MEDIUM POSITIONAL	0.19	0.5
2	1	Z	1316	MEDIUM POSITIONAL	0.19	0.5
2	15	B	1316	MEDIUM POSITIONAL	0.19	0.5
2	1	D	1316	MEDIUM POSITIONAL	0.2	0.5
2	16	F	1316	MEDIUM POSITIONAL	0.19	0.5
2	1	B	1203	LOOSE POSITIONAL	0.41	5
2	14	D	1203	LOOSE POSITIONAL	0.37	5
2	1	F	1203	LOOSE POSITIONAL	0.37	5
2	15	H	1203	LOOSE POSITIONAL	0.38	5
2	1	J	1203	LOOSE POSITIONAL	0.36	5
2	16	L	1203	LOOSE POSITIONAL	0.44	5
2	1	N	1203	LOOSE POSITIONAL	0.39	5
2	1	P	1203	LOOSE POSITIONAL	0.36	5
2	1	R	1203	LOOSE POSITIONAL	0.35	5
2	1	T	1203	LOOSE POSITIONAL	0.38	5
2	1	V	1203	LOOSE POSITIONAL	0.35	5
2	14	X	1203	LOOSE POSITIONAL	0.35	5
2	1	Z	1203	LOOSE POSITIONAL	0.4	5
2	15	B	1203	LOOSE POSITIONAL	0.41	5
2	1	D	1203	LOOSE POSITIONAL	0.38	5
2	16	F	1203	LOOSE POSITIONAL	0.38	5
2	1	B	1316	MEDIUM THERMAL	1.71	2
2	14	D	1316	MEDIUM THERMAL	1.74	2
2	1	F	1316	MEDIUM THERMAL	1.72	2
2	15	H	1316	MEDIUM THERMAL	1.53	2
2	1	J	1316	MEDIUM THERMAL	1.61	2
2	16	L	1316	MEDIUM THERMAL	1.68	2
2	1	N	1316	MEDIUM THERMAL	1.68	2
2	1	P	1316	MEDIUM THERMAL	1.41	2
2	1	R	1316	MEDIUM THERMAL	1.57	2
2	1	T	1316	MEDIUM THERMAL	1.52	2
2	1	V	1316	MEDIUM THERMAL	1.75	2
2	14	X	1316	MEDIUM THERMAL	1.62	2
2	1	Z	1316	MEDIUM THERMAL	1.76	2
2	15	B	1316	MEDIUM THERMAL	1.57	2
2	1	D	1316	MEDIUM THERMAL	1.77	2
2	16	F	1316	MEDIUM THERMAL	1.8	2
2	1	B	1203	LOOSE THERMAL	2.61	10
2	14	D	1203	LOOSE THERMAL	2.57	10
2	1	F	1203	LOOSE THERMAL	2.49	10
2	15	H	1203	LOOSE THERMAL	2.31	10
2	1	J	1203	LOOSE THERMAL	2.43	10
2	16	L	1203	LOOSE THERMAL	2.31	10
2	1	N	1203	LOOSE THERMAL	2.27	10
2	1	P	1203	LOOSE THERMAL	2.41	10
2	1	R	1203	LOOSE THERMAL	2.4	10
2	1	T	1203	LOOSE THERMAL	2.44	10
2	1	V	1203	LOOSE THERMAL	2.49	10
2	14	X	1203	LOOSE THERMAL	2.43	10
2	1	Z	1203	LOOSE THERMAL	2.46	10
2	15	B	1203	LOOSE THERMAL	2.57	10
2	1	D	1203	LOOSE THERMAL	2.35	10
2	16	F	1203	LOOSE THERMAL	2.37	10

LS refinement shell

Resolution: 3.011→3.089 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.374	888	-
R_work	0.295	17435	-
all	-	18323	-
obs	-	-	92.79 %

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	0.5213	-0.0976	-0.1423	1.4925	0.1429	0.9317	0.0475	0.1027	-0.0085	-0.1135	-0.1466	0.1159	0.1586	-0.08	0.099	-0.2762	0.0156	0.0506	-0.1629	-0.0095	-0.1892	-15.0747	3.0171	-73.0429
2	0.5394	-0.2626	0.0215	1.2235	0.0733	0.931	0.0975	0.0991	-0.0458	-0.1011	-0.1479	-0.0383	-0.0976	0.0281	0.0504	-0.3138	0.005	-0.0382	-0.1617	-0.0318	-0.1409	-51.6129	-55.1121	-70.0591
3	0.5755	0.1606	0.0557	1.288	-0.0254	1.1323	0.1222	-0.1564	-0.0549	0.1337	-0.1625	0.0211	-0.1357	-0.0407	0.0403	-0.1187	-0.0196	-0.058	-0.1349	0.0316	-0.1615	-74.5038	8.0999	-19.3338
4	0.4403	0.3092	-0.0409	1.5588	-0.1383	1.0111	0.1071	-0.0945	-0.0089	0.177	-0.1883	-0.2667	-0.0062	0.0801	0.0812	-0.2162	0.0343	0.0319	-0.1462	0.0247	-0.1045	8.0227	-62.2422	-22.9403
5	0.551	0.1322	0.1288	1.4049	0.0888	0.9101	0.0313	-0.0981	0.0025	0.1049	-0.1372	0.12	-0.1763	-0.0711	0.1059	-0.2076	0.0016	-0.0355	-0.1578	-0.0092	-0.2062	-74.6436	-64.5793	-132.5271
6	0.5498	0.2507	-0.0046	1.2228	0.0414	0.8793	0.0894	-0.0979	0.0482	0.082	-0.1277	-0.0144	0.1285	0.0372	0.0383	-0.2552	0.006	0.0541	-0.1517	-0.0322	-0.163	8.0725	-6.4985	-135.4751
7	0.4416	-0.3479	0.0503	1.5268	-0.1565	0.9495	0.1035	0.1095	0.0017	-0.1747	-0.186	-0.2763	-0.0031	0.0738	0.0825	-0.1374	-0.061	-0.0505	-0.1408	0.0259	-0.1222	-51.4614	0.5918	-182.6785
8	0.6002	-0.1415	-0.0756	1.2492	0.0306	1.1077	0.1134	0.161	0.0562	-0.1111	-0.1587	0.0163	0.1253	-0.0472	0.0453	-0.0493	-0.0008	0.0334	-0.134	0.0308	-0.1823	-14.6589	-69.6857	-186.212

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 361
2	X-RAY DIFFRACTION	1	B	1 - 329
3	X-RAY DIFFRACTION	1	C	0 - 361
4	X-RAY DIFFRACTION	1	D	1 - 329
5	X-RAY DIFFRACTION	2	E	0 - 361
6	X-RAY DIFFRACTION	2	F	1 - 329
7	X-RAY DIFFRACTION	2	G	0 - 361
8	X-RAY DIFFRACTION	2	H	1 - 329
9	X-RAY DIFFRACTION	3	I	0 - 361
10	X-RAY DIFFRACTION	3	J	1 - 329
11	X-RAY DIFFRACTION	3	K	0 - 361
12	X-RAY DIFFRACTION	3	L	1 - 329
13	X-RAY DIFFRACTION	4	M	0 - 361
14	X-RAY DIFFRACTION	4	N	1 - 329
15	X-RAY DIFFRACTION	4	O	0 - 361
16	X-RAY DIFFRACTION	4	P	1 - 329
17	X-RAY DIFFRACTION	5	Q	0 - 361
18	X-RAY DIFFRACTION	5	R	1 - 329
19	X-RAY DIFFRACTION	5	S	0 - 361
20	X-RAY DIFFRACTION	5	T	1 - 329
21	X-RAY DIFFRACTION	6	U	0 - 361
22	X-RAY DIFFRACTION	6	V	1 - 329
23	X-RAY DIFFRACTION	6	W	0 - 361
24	X-RAY DIFFRACTION	6	X	1 - 329
25	X-RAY DIFFRACTION	7	Y	0 - 361
26	X-RAY DIFFRACTION	7	Z	1 - 329
27	X-RAY DIFFRACTION	7	1	0 - 361
28	X-RAY DIFFRACTION	7	2	1 - 329
29	X-RAY DIFFRACTION	8	3	0 - 361
30	X-RAY DIFFRACTION	8	4	1 - 329
31	X-RAY DIFFRACTION	8	5	0 - 361
32	X-RAY DIFFRACTION	8	6	1 - 329

-
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