PDB-3tby: CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY ...

ID or keywords:

Entry

Database: PDB / ID: 3tby

Title

CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH THE LCMV-DERIVED GP33 ALTERED PEPTIDE ligand (V3P, Y4F)

Components

Beta-2-microglobulin
GLYCOPROTEIN GPC
H-2 class I histocompatibility antigen, D-B alpha chain

Keywords

Immune system/agonist / Murine MHC / LCMV / receptor binding / Beta2-microglobulin / Immune system / T cell recognition / antigen presentation / altered peptide ligand / agonism / antagonism / T cell receptor / CD8 / Cell Surface / Immune system-agonist complex

Function / homology

Function and homology information

Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / receptor-mediated endocytosis of virus by host cell ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / receptor-mediated endocytosis of virus by host cell / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / iron ion transport / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / host cell endoplasmic reticulum membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function

Biological species

Mus musculus (house mouse)

Lymphocytic choriomeningitis virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Duru, A.D. / Allerbring, E.B. / Uchtenhagen, H. / Mazumdar, P.A. / Badia-Martinez, D. / Madhurantakam, C. / Sandalova, T. / Nygren, P. / Achour, A.

Citation

Journal: To be Published
Title: Conversion of a T cell viral antagonist into an agonist through higher stabilization and conserved molecular mimicry: Implications for TCR recognition
Authors: Duru, A.D. / Allerbring, E.B. / Uchtenhagen, H. / Mazumdar, P.A. / Badia-Martinez, D. / Madhurantakam, C. / Sandalova, T. / Nygren, P. / Achour, A.

History

Deposition	Aug 8, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 8, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3tby.cif.gz	610.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3tby_validation.pdf.gz	502.7 KB	Display	wwPDB validaton report
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Data in CIF	3tby_validation.cif.gz	75.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tb/3tby ftp://data.pdbj.org/pub/pdb/validation_reports/tb/3tby	HTTPS FTP

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Related structure data

Related structure data	3tbsC 3tbtC 3tbvC 3tbwC 1s7uS 1s7v 1s7w 1s7x 3quk 3qul 4nsk S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3tbs-1 1hhh-d 2ve6-1 4prb-d 6vb7-d 4wdi-1 1ktl-2 3cc5-2 6gb7-4 2bsr-d 6vb4-d 1fg2-2 1zhb-4 3tbv-4 6wzy-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) 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

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#62 - Feb 2005 Major Histocompatibility Complex similarity (10) #63 - Mar 2005 T-Cell Receptor similarity (10) #21 - Sep 2001 Antibodies similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #88 - Apr 2007 Clathrin similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #166 - Oct 2013 Proteasome similarity (1) #176 - Aug 2014 Dynein similarity (1) #177 - Sep 2014 Apoptosomes similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#62 - Feb 2005
Major Histocompatibility Complex
similarity (10)
#63 - Mar 2005
T-Cell Receptor
similarity (10)
#21 - Sep 2001
Antibodies
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#88 - Apr 2007
Clathrin
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#166 - Oct 2013
Proteasome
similarity (1)
#176 - Aug 2014
Dynein
similarity (1)
#177 - Sep 2014
Apoptosomes
similarity (1)

Deposited unit

A: H-2 class I histocompatibility antigen, D-B alpha chain

B: Beta-2-microglobulin

C: GLYCOPROTEIN GPC

D: H-2 class I histocompatibility antigen, D-B alpha chain

E: Beta-2-microglobulin

F: GLYCOPROTEIN GPC

G: H-2 class I histocompatibility antigen, D-B alpha chain

H: Beta-2-microglobulin

I: GLYCOPROTEIN GPC

J: H-2 class I histocompatibility antigen, D-B alpha chain

K: Beta-2-microglobulin

L: GLYCOPROTEIN GPC

179 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: H-2 class I histocompatibility antigen, D-B alpha chain

B: Beta-2-microglobulin

C: GLYCOPROTEIN GPC

defined by author&software
44.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: H-2 class I histocompatibility antigen, D-B alpha chain

E: Beta-2-microglobulin

F: GLYCOPROTEIN GPC

defined by author&software
44.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: H-2 class I histocompatibility antigen, D-B alpha chain

H: Beta-2-microglobulin

I: GLYCOPROTEIN GPC

defined by author&software
44.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: H-2 class I histocompatibility antigen, D-B alpha chain

K: Beta-2-microglobulin

L: GLYCOPROTEIN GPC

defined by author&software
44.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.820, 124.270, 99.650
Angle α, β, γ (deg.)	90.00, 103.29, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLY	GLY	GLU	GLU	3	A	A	1 - 154	1 - 154
2	1	GLY	GLY	GLU	GLU	3	D	D	1 - 154	1 - 154
3	1	GLY	GLY	GLU	GLU	3	G	G	1 - 154	1 - 154
4	1	GLY	GLY	GLU	GLU	3	J	J	1 - 154	1 - 154
1	2	TYR	TYR	LYS	LYS	3	A	A	156 - 173	156 - 173
2	2	TYR	TYR	LYS	LYS	3	D	D	156 - 173	156 - 173
3	2	TYR	TYR	LYS	LYS	3	G	G	156 - 173	156 - 173
4	2	TYR	TYR	LYS	LYS	3	J	J	156 - 173	156 - 173
1	3	ILE	ILE	MET	MET	2	B	B	1 - 99	1 - 99
2	3	ILE	ILE	MET	MET	2	E	E	1 - 99	1 - 99
3	3	ILE	ILE	MET	MET	2	H	H	1 - 99	1 - 99
4	3	ILE	ILE	MET	MET	2	K	K	1 - 99	1 - 99
1	4	LEU	LEU	ARG	ARG	3	A	A	180 - 273	180 - 273
2	4	LEU	LEU	ARG	ARG	3	D	D	180 - 273	180 - 273
3	4	LEU	LEU	ARG	ARG	3	G	G	180 - 273	180 - 273
4	4	LEU	LEU	ARG	ARG	3	J	J	180 - 273	180 - 273

NCS ensembles :

ID
1
2
3
4

#1: Protein	H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B) Mass: 32087.703 Da / Num. of mol.: 4 / Fragment: RESIDUES 25-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1, H2-DB / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899
#2: Protein	Beta-2-microglobulin Mass: 11704.359 Da / Num. of mol.: 4 / Fragment: RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide	GLYCOPROTEIN GPC Mass: 1027.215 Da / Num. of mol.: 4 / Fragment: RESIDUES 33-41 / Mutation: V35P,Y36F / Source method: obtained synthetically Details: LYMPHOCYTIC CHORIOMENINGITIS VIRUS glycoprotein GPC Source: (synth.) Lymphocytic choriomeningitis virus / References: UniProt: P07399
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.12 Å³/Da / Density % sol: 60.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Crystals were obtained in 1.6-1.8 M ammonium sulfate, 0.1 M Tris HCl pH 7.0-9.0 screening conditions. 4 ul of a 5mg/ml protein solution were mixed in a 4:2 ratio with the crystallization ...Details: Crystals were obtained in 1.6-1.8 M ammonium sulfate, 0.1 M Tris HCl pH 7.0-9.0 screening conditions. 4 ul of a 5mg/ml protein solution were mixed in a 4:2 ratio with the crystallization reservoir , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal

Density Matthews: 3.12 Å³/Da / Density % sol: 60.58 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystals were obtained in 1.6-1.8 M ammonium sulfate, 0.1 M Tris HCl pH 7.0-9.0 screening conditions. 4 ul of a 5mg/ml protein solution were mixed in a 4:2 ratio with the crystallization ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 25, 2008
Radiation	Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.934 Å / Relative weight: 1
Reflection	Resolution: 2.5→48.5 Å / Num. all: 75693 / Num. obs: 75693 / % possible obs: 98.1 % / Redundancy: 3.7 % / B_iso Wilson estimate: 55.1 Å² / R_merge(I) obs: 0.112 / Net I/σ(I): 10.7
Reflection shell	Resolution: 2.5→2.65 Å / R_merge(I) obs: 0.631 / Mean I/σ(I) obs: 1.9 / Num. unique all: 11100 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
MOLREP		phasing
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1S7U

1s7u

Resolution: 2.5→20 Å / Cor.coef. F_o:F_c: 0.854 / Cor.coef. F_o:F_c free: 0.826 / SU B: 29.388 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.31473	3749	5 %	RANDOM
R_work	0.28449	-	-	-
all	0.28604	70600	-	-
obs	0.28604	70600	97.9 %	-

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: 38.631 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	0 Å²	-0.87 Å²
2-	-	0.1 Å²	0 Å²
3-	-	-	-0.38 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12264	0	0	232	12496

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.021	12684
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8752
X-RAY DIFFRACTION	r_angle_refined_deg	1.192	1.935	17220
X-RAY DIFFRACTION	r_angle_other_deg	0.817	3	21100
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.345	5	1472
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.045	23.494	664
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.503	15	2060
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.293	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1728
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	14108
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2720
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	0.262	1.5	7472
X-RAY DIFFRACTION	r_mcbond_other	0.076	1.5	2976
X-RAY DIFFRACTION	r_mcangle_it	0.482	2	12044
X-RAY DIFFRACTION	r_scbond_it	0.814	3	5212
X-RAY DIFFRACTION	r_scangle_it	1.254	4.5	5176
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	903	TIGHT POSITIONAL	0.03	0.05
1	2	D	903	TIGHT POSITIONAL	0.03	0.05
1	3	G	903	TIGHT POSITIONAL	0.03	0.05
1	4	J	903	TIGHT POSITIONAL	0.03	0.05
1	1	A	1287	LOOSE POSITIONAL	0.03	5
1	2	D	1287	LOOSE POSITIONAL	0.03	5
1	3	G	1287	LOOSE POSITIONAL	0.03	5
1	4	J	1287	LOOSE POSITIONAL	0.03	5
1	1	A	903	TIGHT THERMAL	0.06	0.5
1	2	D	903	TIGHT THERMAL	0.06	0.5
1	3	G	903	TIGHT THERMAL	0.06	0.5
1	4	J	903	TIGHT THERMAL	0.06	0.5
1	1	A	1287	LOOSE THERMAL	0.06	10
1	2	D	1287	LOOSE THERMAL	0.06	10
1	3	G	1287	LOOSE THERMAL	0.07	10
1	4	J	1287	LOOSE THERMAL	0.06	10
2	1	A	107	TIGHT POSITIONAL	0.03	0.05
2	2	D	107	TIGHT POSITIONAL	0.03	0.05
2	3	G	107	TIGHT POSITIONAL	0.03	0.05
2	4	J	107	TIGHT POSITIONAL	0.03	0.05
2	1	A	173	LOOSE POSITIONAL	0.02	5
2	2	D	173	LOOSE POSITIONAL	0.02	5
2	3	G	173	LOOSE POSITIONAL	0.03	5
2	4	J	173	LOOSE POSITIONAL	0.02	5
2	1	A	107	TIGHT THERMAL	0.05	0.5
2	2	D	107	TIGHT THERMAL	0.06	0.5
2	3	G	107	TIGHT THERMAL	0.07	0.5
2	4	J	107	TIGHT THERMAL	0.06	0.5
2	1	A	173	LOOSE THERMAL	0.06	10
2	2	D	173	LOOSE THERMAL	0.1	10
2	3	G	173	LOOSE THERMAL	0.06	10
2	4	J	173	LOOSE THERMAL	0.08	10
3	1	B	582	TIGHT POSITIONAL	0.21	0.05
3	2	E	582	TIGHT POSITIONAL	0.2	0.05
3	3	H	582	TIGHT POSITIONAL	0.17	0.05
3	4	K	582	TIGHT POSITIONAL	0.22	0.05
3	1	B	813	MEDIUM POSITIONAL	0.28	0.5
3	2	E	813	MEDIUM POSITIONAL	0.26	0.5
3	3	H	813	MEDIUM POSITIONAL	0.27	0.5
3	4	K	813	MEDIUM POSITIONAL	0.29	0.5
3	1	B	582	TIGHT THERMAL	0.31	0.5
3	2	E	582	TIGHT THERMAL	0.32	0.5
3	3	H	582	TIGHT THERMAL	0.32	0.5
3	4	K	582	TIGHT THERMAL	0.35	0.5
3	1	B	813	MEDIUM THERMAL	0.49	2
3	2	E	813	MEDIUM THERMAL	0.43	2
3	3	H	813	MEDIUM THERMAL	0.44	2
3	4	K	813	MEDIUM THERMAL	0.43	2
4	1	A	497	TIGHT POSITIONAL	0.02	0.05
4	2	D	497	TIGHT POSITIONAL	0.02	0.05
4	3	G	497	TIGHT POSITIONAL	0.02	0.05
4	4	J	497	TIGHT POSITIONAL	0.02	0.05
4	1	A	663	LOOSE POSITIONAL	0.02	5
4	2	D	663	LOOSE POSITIONAL	0.02	5
4	3	G	663	LOOSE POSITIONAL	0.02	5
4	4	J	663	LOOSE POSITIONAL	0.02	5
4	1	A	497	TIGHT THERMAL	0.03	0.5
4	2	D	497	TIGHT THERMAL	0.03	0.5
4	3	G	497	TIGHT THERMAL	0.04	0.5
4	4	J	497	TIGHT THERMAL	0.03	0.5
4	1	A	663	LOOSE THERMAL	0.03	10
4	2	D	663	LOOSE THERMAL	0.04	10
4	3	G	663	LOOSE THERMAL	0.04	10
4	4	J	663	LOOSE THERMAL	0.03	10

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.395	264	-
R_work	0.369	5181	-
obs	-	-	99.07 %

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	3.6942	1.1452	0.5125	6.5693	0.04	2.5447	-0.0253	-0.0689	0.3666	0.1476	-0.0006	0.4064	-0.2947	-0.1273	0.026	0.1048	0.1015	0.0427	0.2783	-0.0119	0.087	40.256	5.859	29.829
2	3.9087	2.0515	1.0872	2.3741	2.071	10.8089	0.1361	0.2934	-0.1105	0.0816	-0.1641	0.272	-0.173	-0.2117	0.0281	0.2258	0.1033	0.0103	0.3467	-0.0128	0.3407	28.764	3.863	37.184
3	5.0152	0.4457	-2.3706	0.3005	-0.0908	2.3665	0.3189	-0.3392	0.2762	0.1391	-0.1346	-0.0077	-0.5151	-0.0181	-0.1843	0.2305	-0.0011	0.0293	0.1027	-0.0108	0.1556	53.827	8.737	33.971
4	5.1322	6.0033	-0.6042	8.4992	-0.4387	0.1511	-0.0737	-0.0563	-0.5478	-0.1541	-0.0929	-0.2185	0.041	-0.0729	0.1667	0.1481	-0.0085	0.0736	0.2927	-0.0037	0.2296	41.984	-11.409	31.583
5	2.3742	0.6961	-1.128	1.7151	-0.7293	2.655	0.002	-0.1183	-0.2697	0.0692	-0.0785	-0.1926	0.2857	0.0423	0.0764	0.0808	0.0027	0.0301	0.0976	0.0009	0.1254	57.732	-5.883	30.43
6	5.1915	0.8925	1.2141	2.5235	-0.0645	1.2814	0.1682	-0.3627	-0.1826	0.1262	-0.1017	0.2293	0.0192	-0.2778	-0.0664	0.1565	0.0331	0.0959	0.22	-0.0162	0.136	44.535	-7.833	39.549
7	0.3115	0.6854	-1.4737	2.9915	-1.4071	10.8117	0.1314	0.0307	0.0796	-0.0612	0.2005	0.1736	-0.5478	-0.3848	-0.332	0.4061	0.0416	-0.0006	0.4799	0.0082	0.5512	25.827	-8.052	7.467
8	2.5027	-1.2685	-0.7984	1.529	0.486	7.414	-0.1138	-0.0053	-0.2898	-0.5568	0.303	0.1781	-0.1	-0.0236	-0.1892	0.4814	-0.1232	0.0254	0.2495	0.036	0.3688	32.007	-10.024	2.419
9	1.0585	-0.5949	0.1718	2.3465	-1.2716	0.7346	-0.3742	-0.0018	-0.6331	-1.0055	0.1296	-0.3715	0.6915	-0.0992	0.2446	1.0054	0.0417	0.4006	0.5121	-0.2957	1.0943	39.386	-11.65	0.703
10	2.1946	0.424	-1.2903	2.5343	-0.1974	0.7825	-0.2411	0.439	-0.3639	-0.8815	0.0478	0.3848	0.1378	-0.346	0.1934	0.4971	-0.0475	-0.1003	0.4325	0.0621	0.4174	29.647	-12.286	0.601
11	5.5269	-1.6467	2.3146	1.9944	-1.3735	2.8533	0.0154	-0.162	-0.0046	-0.0151	0.0447	0.1161	-0.0008	-0.1678	-0.0602	0.0972	0.048	0.082	0.1294	0.0013	0.1146	34.812	5.481	6.837
12	0.808	-0.7956	1.2976	0.9048	-1.4894	2.7304	-0.3004	-0.2534	0.3019	0.2297	0.1611	-0.225	-0.4735	-0.4635	0.1393	0.2879	0.1746	-0.0132	0.303	-0.0059	0.3491	38.913	14.058	12.134
13	3.7067	-2.3693	3.6903	2.4425	-3.1801	4.6761	-0.0559	-0.1311	-0.0997	-0.0791	0.2903	0.2261	-0.1062	-0.38	-0.2343	0.1847	0.0096	0.0305	0.1754	-0.0253	0.1273	34.552	8.029	8.804
14	3.8002	1.0738	2.6366	5.1923	0.2907	5.7247	-0.0991	0.1269	0.4022	0.0554	0.1522	-0.0399	0.0734	0.1784	-0.0531	0.1843	0.0512	0.0822	0.2479	0.0203	0.1469	42.112	10.607	2.762
15	7.2831	-5.8462	0.6988	7.0877	-2.9545	2.8579	-0.2145	-0.0264	0.782	0.2411	0.269	-0.7772	-0.1518	-0.0329	-0.0545	0.0682	-0.0851	-0.0139	0.2158	-0.1354	0.3065	-6.416	0.97	20.847
16	5.111	-0.9418	-0.5987	11.7243	1.1114	1.9647	0.0799	0.3968	0.3178	-0.2821	-0.0327	-0.2994	-0.4069	0.1945	-0.0472	0.1171	-0.0813	0.0431	0.2749	-0.039	0.0658	-0.971	6.059	18.535
17	5.7055	-1.3206	2.8403	5.2	-5.1023	7.5342	-0.0215	0.2319	-0.0678	-0.1934	-0.0485	-0.422	-0.2885	0.5582	0.07	0.1901	-0.009	0.0492	0.3158	-0.0445	0.3481	8.498	1.384	12.273
18	4.9036	-0.6705	-2.3902	0.6441	-0.5754	2.842	0.2318	0.1977	0.3353	-0.02	-0.0371	0.0107	-0.3625	-0.0088	-0.1947	0.2986	-0.0688	-0.0145	0.1005	-0.0156	0.1434	-16.218	8.051	14.975
19	2.7554	-4.781	-1.5225	9.6165	2.5666	0.9407	-0.0955	-0.1281	-0.3076	0.1056	0.0183	0.1883	0.1293	0.1351	0.0772	0.1217	0.005	-0.0272	0.1755	-0.0272	0.2759	-5.904	-12.904	17.492
20	1.6176	0.9536	0.0085	2.8157	-0.2445	2.5449	0.0102	0.035	-0.1691	-0.0288	-0.0681	0.0909	0.2676	-0.1452	0.0579	0.0378	-0.0024	0.027	0.072	-0.0111	0.1034	-21.24	-6.249	18.33
21	8.1145	-1.5379	1.5494	3.0285	-0.0818	2.5947	0.1252	0.3091	-0.2991	0.0328	-0.0607	-0.2644	0.1251	0.2564	-0.0644	0.1583	0.0042	0.0808	0.1333	-0.0213	0.1044	-6.091	-9.349	10.536
22	1.1884	0.8621	-0.3024	2.3175	-0.4289	5.3659	-0.0717	-0.1218	-0.0614	0.1694	-0.0063	-0.1497	0.0376	0.7189	0.0779	0.3247	0.0554	-0.0672	0.3034	0.0033	0.4238	5.443	-12.056	46.454
23	3.7518	1.8084	-9.0235	1.0617	-4.6422	22.3583	0.0346	0.0583	-0.2946	-0.1395	0.0415	0.3814	0.3954	-0.1076	-0.0761	0.5606	-0.2193	-0.2509	0.417	-0.2122	1.6052	-4.404	-13.452	48.162
24	1.8343	0.4552	-0.9896	2.3457	-0.0351	0.5699	-0.1028	-0.5172	-0.2415	0.3853	0.0548	-0.3199	0.1179	0.3524	0.048	0.4345	0.0987	-0.1533	0.424	-0.0478	0.4343	5.212	-15.137	48.41
25	7.419	-0.0041	2.6692	2.8491	-0.3161	2.0499	-0.0249	-0.0891	-0.3324	0.1121	0.0394	-0.2737	0.0572	0.2034	-0.0146	0.144	-0.0218	0.0758	0.1892	-0.0275	0.0976	1.979	3.23	42.402
26	1.9498	1.5296	2.0699	1.5104	1.729	2.2366	-0.3343	0.3164	0.2945	-0.1592	0.1013	0.054	-0.3424	0.305	0.2329	0.2745	-0.1731	-0.0115	0.2723	0.0005	0.2683	-1.09	12.132	36.96
27	3.1906	1.3118	2.8831	2.0457	1.8832	2.9726	0.1116	0.3183	-0.1664	0.2493	0.1972	-0.3725	0.1471	0.4226	-0.3088	0.1637	-0.063	0.0554	0.3088	-0.0266	0.1725	2.564	5.727	40.408
28	1.3528	0.2421	2.2544	4.3166	-0.6786	5.1402	-0.1268	-0.305	0.187	0.1063	0.0664	-0.0909	-0.3705	-0.0963	0.0604	0.2599	-0.0132	0.0705	0.2742	-0.1207	0.1698	-4.805	9.148	46.305
29	4.0072	1.7465	0.1785	5.0841	-0.1097	2.2603	0.1313	-0.0027	-0.4434	0.2172	-0.0948	-0.5761	0.2199	0.1346	-0.0364	0.123	0.1128	0.0067	0.1931	-0.0158	0.1672	-5.98	-49.29	31.812
30	4.9739	2.529	-7.234	4.3047	-5.0121	11.1385	0.0137	-0.5976	-0.156	0.3143	-0.4918	-0.7343	-0.0637	1.0057	0.4781	0.3887	0.0659	-0.1886	0.3279	-0.0125	0.5418	4.774	-47.528	40.25
31	8.3393	-0.5865	4.9388	0.7332	-0.3626	5.0655	0.1276	-0.4748	-0.3422	0.2894	-0.0002	-0.1765	0.3175	-0.269	-0.1275	0.2728	0.0113	0.0221	0.038	0.0584	0.1737	-19.91	-52.033	34.607
32	6.1733	6.9534	2.4417	8.0047	3.0533	1.6303	-0.0795	-0.093	0.2353	-0.2087	-0.0258	0.1722	-0.3146	0.1018	0.1053	0.2081	0.0521	-0.0314	0.1765	-0.0149	0.3387	-7.649	-32.015	33.587
33	3.4202	-0.5974	0.4418	2.9094	0.848	3.0014	-0.1888	-0.0253	0.2867	0.0055	-0.0591	0.1689	-0.1658	0.008	0.248	0.0823	0.0517	0.0167	0.0426	0.0275	0.0751	-23.299	-37.319	30.891
34	6.8246	1.4389	-0.5809	2.2359	0.2074	1.5979	-0.1064	-0.4967	0.3868	0.1404	0.0378	-0.3551	-0.1084	0.332	0.0685	0.2803	0.0409	-0.0291	0.1223	0.0044	0.184	-9.442	-35.565	40.62
35	2.8239	-0.0104	-0.3504	3.3687	1.5463	1.8748	0.1458	0.3425	-0.0932	-0.0354	0.1039	-0.2044	0.6672	0.4183	-0.2498	0.564	0.1203	-0.0439	0.4324	-0.0283	0.5787	9.382	-35.017	6.552
36	1.6263	0.6578	-1.0879	4.9979	-2.5951	7.6162	-0.0211	0.2512	0.0375	-0.5284	0.2071	0.3214	0.0716	-0.0395	-0.1859	0.2503	0.0209	0.031	0.2559	-0.0734	0.3836	4.814	-33.199	6.682
37	1.1382	-1.8516	3.0236	3.5602	-5.5187	8.9311	0.1491	0.236	0.134	0.0933	-0.0815	0.3529	-0.4108	0.4347	-0.0676	0.9853	-0.0053	-0.0265	0.4597	0.1872	1.1153	-2.547	-31.807	3.11
38	2.2955	0.9663	0.672	2.9942	-0.3364	1.5414	-0.1118	0.4137	0.3472	-0.6459	0.0128	-0.2939	-0.3471	0.3666	0.099	0.386	0.0414	0.0835	0.3838	-0.0976	0.3638	7.147	-30.912	4.072
39	7.4404	-1.8452	-0.8137	1.7821	1.1876	2.0576	-0.1963	0.1828	0.193	0.0538	0.132	-0.1862	0.0528	0.1084	0.0643	0.1305	0.0296	0.027	0.0803	0.0106	0.1012	1.731	-48.925	9.738
40	0.2492	0.0413	-0.5909	0.0224	-0.0546	1.552	-0.2189	-0.0809	-0.1615	0.0166	0.0111	-0.0779	0.669	0.2126	0.2079	0.3839	0.1362	-0.0115	0.1684	-0.0105	0.3574	-2.73	-57.48	14.799
41	3.8955	-1.2669	-2.7595	1.603	0.8327	2.2534	-0.1455	-0.261	-0.0115	-0.0986	0.1872	-0.1957	0.259	0.3688	-0.0416	0.1298	0.0767	0.0227	0.194	-0.0204	0.1315	1.846	-51.426	11.798
42	12.8077	3.6625	-5.8951	2.1998	-1.525	4.7198	-0.0698	0.2965	-0.087	-0.0868	0.1777	0.1374	0.2733	0.005	-0.1078	0.2074	0.023	0.015	0.1319	-0.0469	0.1542	-5.009	-54.338	5.065
43	8.6357	-6.3626	1.1494	8.8018	-0.2555	3.5464	0.0597	0.2709	-0.2913	0.176	-0.0765	0.572	0.1292	-0.075	0.0169	0.1051	-0.1137	0.0551	0.2047	-0.0167	0.0877	41.637	-44.195	18.154
44	4.7778	-2.8046	1.5252	9.6274	-1.2843	2.1419	0.088	0.3102	-0.402	-0.11	-0.1424	0.5057	0.3293	-0.2594	0.0543	0.1163	-0.1069	0.0569	0.2511	0.0111	0.1873	36.642	-49.318	15.07
45	2.8904	-2.8984	0.8844	5.5441	1.0313	3.7791	0.0471	0.3861	-0.0863	-0.3616	-0.2818	0.5242	0.0121	-0.6797	0.2346	0.2958	-0.0915	-0.0496	0.4244	-0.019	0.4466	27.87	-44.634	7.859
46	6.3288	-0.4858	2.976	1.2068	-0.2479	2.8144	0.1746	0.3116	-0.3684	-0.3044	-0.0624	0.1693	0.4972	0.1371	-0.1122	0.2611	-0.0153	0.0465	0.0674	-0.0442	0.1291	52.234	-50.916	13.281
47	4.5255	-6.5247	0.9205	10.3613	-1.4811	0.2346	-0.0651	0.2596	0.3792	0.4667	-0.0297	-0.249	-0.117	-0.012	0.0948	0.2641	0.0826	0.012	0.2533	0.0596	0.3134	41.238	-30.25	15.172
48	1.41	-0.0226	0.1998	3.4969	-0.5309	1.8889	-0.1706	0.0724	0.3048	-0.0135	0.014	-0.1979	-0.1759	-0.1154	0.1566	0.0713	-0.0195	-0.017	0.0413	-0.0023	0.1	56.508	-36.617	17.657
49	4.1325	-1.6955	-0.7638	2.7849	0.3895	2.4856	0.0859	0.3567	0.1986	0.0382	-0.0906	0.3674	-0.0669	-0.4454	0.0048	0.212	-0.0425	0.0045	0.1373	0.0156	0.1724	42.348	-33.569	8.277
50	0.9787	0.3446	-0.8939	3.7858	0.0653	1.1615	0.2603	-0.2509	0.0146	0.4078	0.0326	0.1579	-0.0911	-0.0078	-0.2929	0.3953	-0.0739	0.0113	0.5649	0.0144	0.5811	27.549	-31.701	43.232
51	1.9769	0.5477	-4.5072	0.1534	-1.2457	10.3409	0.2434	-0.4487	0.1257	0.0731	-0.1002	0.0315	-0.6054	1.1742	-0.1432	0.6801	-0.1081	-0.3277	0.9575	-0.162	0.8755	37.158	-30.551	46.067
52	1.904	-0.6108	-0.341	0.8289	0.0294	0.0859	0.0819	-0.3823	0.3491	0.5481	-0.005	0.0973	-0.112	0.0107	-0.0769	0.6121	-0.0505	0.0554	0.5134	-0.0502	0.511	27.639	-28.655	45.257
53	14.5172	0.5835	-4.8322	1.7707	-0.9182	4.1624	-0.0522	-0.1532	0.262	0.0064	0.1062	0.1588	-0.0239	-0.1315	-0.0541	0.1715	-0.0449	0.0172	0.1212	-0.0076	0.1384	31.333	-47.466	38.895
54	0.9001	-0.0697	-0.8222	0.1602	0.0145	0.7718	-0.3323	0.1392	-0.296	-0.1539	0.0997	0.0515	0.3697	-0.1728	0.2325	0.3632	-0.1466	0.0185	0.3119	0.0475	0.3241	34.631	-55.939	32.901
55	4.0398	0.5812	-3.5304	1.2936	-1.432	3.8226	-0.0637	0.221	0.0418	0.0345	0.2498	0.2648	0.056	-0.442	-0.186	0.1116	-0.079	0.0534	0.2921	-0.0413	0.1774	30.839	-49.753	36.625
56	7.9521	-1.6899	-3.8369	3.4521	0.9665	5.2234	-0.2217	-0.0563	-0.1173	0.1575	0.1508	-0.2496	0.1767	0.0687	0.0709	0.203	-0.0925	-0.0195	0.233	0.027	0.2368	37.681	-53.912	42.713

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 44
2	X-RAY DIFFRACTION	2	A	45 - 62
3	X-RAY DIFFRACTION	3	A	63 - 95
4	X-RAY DIFFRACTION	4	A	96 - 116
5	X-RAY DIFFRACTION	5	A	117 - 142
6	X-RAY DIFFRACTION	6	A	143 - 175
7	X-RAY DIFFRACTION	7	A	176 - 194
8	X-RAY DIFFRACTION	8	A	198 - 218
9	X-RAY DIFFRACTION	9	A	221 - 233
10	X-RAY DIFFRACTION	10	A	234 - 275
11	X-RAY DIFFRACTION	11	B	1 - 29
12	X-RAY DIFFRACTION	12	B	30 - 56
13	X-RAY DIFFRACTION	13	B	57 - 78
14	X-RAY DIFFRACTION	14	B	79 - 99
15	X-RAY DIFFRACTION	15	D	1 - 17
16	X-RAY DIFFRACTION	16	D	18 - 44
17	X-RAY DIFFRACTION	17	D	45 - 62
18	X-RAY DIFFRACTION	18	D	63 - 95
19	X-RAY DIFFRACTION	19	D	96 - 116
20	X-RAY DIFFRACTION	20	D	117 - 142
21	X-RAY DIFFRACTION	21	D	143 - 179
22	X-RAY DIFFRACTION	22	D	180 - 218
23	X-RAY DIFFRACTION	23	D	221 - 233
24	X-RAY DIFFRACTION	24	D	234 - 275
25	X-RAY DIFFRACTION	25	E	1 - 29
26	X-RAY DIFFRACTION	26	E	30 - 56
27	X-RAY DIFFRACTION	27	E	57 - 78
28	X-RAY DIFFRACTION	28	E	79 - 99
29	X-RAY DIFFRACTION	29	G	1 - 44
30	X-RAY DIFFRACTION	30	G	45 - 62
31	X-RAY DIFFRACTION	31	G	63 - 95
32	X-RAY DIFFRACTION	32	G	96 - 116
33	X-RAY DIFFRACTION	33	G	117 - 142
34	X-RAY DIFFRACTION	34	G	143 - 176
35	X-RAY DIFFRACTION	35	G	179 - 198
36	X-RAY DIFFRACTION	36	G	199 - 218
37	X-RAY DIFFRACTION	37	G	221 - 233
38	X-RAY DIFFRACTION	38	G	234 - 275
39	X-RAY DIFFRACTION	39	H	1 - 29
40	X-RAY DIFFRACTION	40	H	30 - 56
41	X-RAY DIFFRACTION	41	H	57 - 78
42	X-RAY DIFFRACTION	42	H	79 - 99
43	X-RAY DIFFRACTION	43	J	1 - 17
44	X-RAY DIFFRACTION	44	J	18 - 44
45	X-RAY DIFFRACTION	45	J	45 - 62
46	X-RAY DIFFRACTION	46	J	63 - 95
47	X-RAY DIFFRACTION	47	J	96 - 116
48	X-RAY DIFFRACTION	48	J	117 - 142
49	X-RAY DIFFRACTION	49	J	143 - 175
50	X-RAY DIFFRACTION	50	J	180 - 218
51	X-RAY DIFFRACTION	51	J	221 - 233
52	X-RAY DIFFRACTION	52	J	234 - 275
53	X-RAY DIFFRACTION	53	K	1 - 29
54	X-RAY DIFFRACTION	54	K	30 - 56
55	X-RAY DIFFRACTION	55	K	57 - 78
56	X-RAY DIFFRACTION	56	K	79 - 99

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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

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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

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Yorodumi