PDB-3rg1: Crystal structure of the RP105/MD-1 complex

ID or keywords:

Entry

Database: PDB / ID: 3rg1

Title

Crystal structure of the RP105/MD-1 complex

Components

CD180 molecule
LY86 protein

Keywords

IMMUNE SYSTEM / leucine-rich repeat domain / beta-cup-like structure / immune regulation

Function / homology

Function and homology information

membrane => GO:0016020 / immune response
Similarity search - Function

Biological species

Bos taurus (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.91 Å

Authors

Yoon, S.I. / Hong, M. / Wilson, I.A.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2011
Title: An unusual dimeric structure and assembly for TLR4 regulator RP105-MD-1.
Authors: Yoon, S.I. / Hong, M. / Wilson, I.A.

History

Deposition	Apr 7, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 31, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 7, 2011	Group: Database references
Revision 1.2	Sep 21, 2011	Group: Database references
Revision 2.0	Jul 29, 2020	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3rg1.cif.gz	2.1 MB	Display	PDBx/mmCIF format
PDB format	pdb3rg1.ent.gz	1.7 MB	Display	PDB format
PDBx/mmJSON format	3rg1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3rg1_validation.pdf.gz	6.4 MB	Display	wwPDB validaton report
Full document	3rg1_full_validation.pdf.gz	6.5 MB	Display
Data in XML	3rg1_validation.xml.gz	193.7 KB	Display
Data in CIF	3rg1_validation.cif.gz	261.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rg/3rg1 ftp://data.pdbj.org/pub/pdb/validation_reports/rg/3rg1	HTTPS FTP

-
Related structure data

Similar structure data	3b2d-d 3t6q-d 7db8-d 3ujp-1 7db7-d 11887 7daw-d 6mzd-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

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (10) #248 - Aug 2020 Phytosulfokine Receptor similarity (6) #68 - Aug 2005 Neurotrophins similarity (4) #105 - Sep 2008 Ribonuclease A similarity (2) #245 - May 2020 Spliceosomes similarity (2)

Deposited unit

A: CD180 molecule

E: CD180 molecule

I: CD180 molecule

M: CD180 molecule

B: CD180 molecule

F: CD180 molecule

J: CD180 molecule

N: CD180 molecule

C: LY86 protein

D: LY86 protein

G: LY86 protein

H: LY86 protein

K: LY86 protein

L: LY86 protein

O: LY86 protein

P: LY86 protein

hetero molecules

702 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CD180 molecule

B: CD180 molecule

C: LY86 protein

D: LY86 protein

hetero molecules

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

2

E: CD180 molecule

F: CD180 molecule

G: LY86 protein

H: LY86 protein

hetero molecules

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

3

I: CD180 molecule

J: CD180 molecule

K: LY86 protein

L: LY86 protein

hetero molecules

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

4

M: CD180 molecule

N: CD180 molecule

O: LY86 protein

P: LY86 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	101.509, 141.577, 141.953
Angle α, β, γ (deg.)	94.00, 91.66, 91.37
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	B	26 - 136
2	1	1	1	F	26 - 136
3	1	1	1	J	26 - 136
4	1	1	1	N	26 - 136
5	1	1	1	A	26 - 136
6	1	1	1	E	26 - 136
7	1	1	1	I	26 - 136
8	1	1	1	M	26 - 136
1	1	2	1	C	21 - 84
2	1	2	1	D	21 - 84
3	1	2	1	H	21 - 84
4	1	2	1	K	21 - 84
5	1	2	1	L	21 - 84
6	1	2	1	O	21 - 84
7	1	2	1	P	21 - 84
8	1	2	1	G	21 - 84
1	2	2	1	C	92 - 123
2	2	2	1	D	92 - 123
3	2	2	1	H	92 - 123
4	2	2	1	K	92 - 123
5	2	2	1	L	92 - 123
6	2	2	1	O	92 - 123
7	2	2	1	P	92 - 123
8	2	2	1	G	92 - 123
1	3	2	1	C	137 - 160
2	3	2	1	D	137 - 160
3	3	2	1	H	137 - 160
4	3	2	1	K	137 - 160
5	3	2	1	L	137 - 160
6	3	2	1	O	137 - 160
7	3	2	1	P	137 - 160
8	3	2	1	G	137 - 160
1	1	3	1	B	137 - 380
2	1	3	1	A	137 - 380
3	1	3	1	E	137 - 380
4	1	3	1	I	137 - 380
5	1	3	1	M	137 - 380
6	1	3	1	F	137 - 380
7	1	3	1	J	137 - 380
8	1	3	1	N	137 - 380
1	1	4	1	B	381 - 490
2	1	4	1	A	381 - 490
3	1	4	1	I	381 - 490
4	1	4	1	M	381 - 490
5	1	4	1	E	381 - 490
6	1	4	1	F	381 - 490
7	1	4	1	J	381 - 490
8	1	4	1	N	381 - 490
1	1	5	1	B	700 - 1000
2	1	5	1	A	700 - 1000
3	1	5	1	E	700 - 1000
4	1	5	1	I	700 - 1000
5	1	5	1	M	700 - 1000
6	1	5	1	F	700 - 1000
7	1	5	1	J	700 - 1000
8	1	5	1	N	700 - 1000
1	1	6	1	D	201
2	1	6	1	H	201
3	1	6	1	L	201
4	1	6	1	P	201
1	1	7	1	B	491 - 536
2	1	7	1	F	491 - 536
3	1	7	1	J	491 - 536
4	1	7	1	N	491 - 536
5	1	7	1	A	491 - 536
6	1	7	1	E	491 - 536
7	1	7	1	I	491 - 536
8	1	7	1	M	491 - 536
1	1	8	1	B	537 - 625
2	1	8	1	F	537 - 625
3	1	8	1	J	537 - 625
4	1	8	1	N	537 - 625
5	1	8	1	A	537 - 625
6	1	8	1	E	537 - 625
7	1	8	1	M	537 - 625

NCS ensembles :

ID
1
2
3
4
5
6
7
8

-
Protein , 2 types, 16 molecules AEIMBFJNCDGHKLOP

#1: Protein	CD180 molecule / RP105 / radioprotective 105 Mass: 68866.977 Da / Num. of mol.: 8 / Fragment: ectodomain (UNP residues 24-626) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: CD180 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A6QNK7
#2: Protein	LY86 protein / MD-1 Mass: 16496.688 Da / Num. of mol.: 8 / Fragment: UNP residues 21-159 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: LY86 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A4IFT3

-
Sugars , 2 types, 16 molecules

#3: Polysaccharide

beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...

Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}	LINUCS	PDB-CARE

#4: Polysaccharide

alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...

Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1_g2-h1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}	LINUCS	PDB-CARE

-
Non-polymers , 2 types, 41 molecules

#5: Chemical	ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT) Mass: 751.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄₀H₇₉O₁₀P / Comment: phospholipid*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Nonpolymer details	THE LIGAND DENOTED AS PGT HAS BEEN CO-PURIFIED ALONG WITH THE PROTEIN AND ITS EXACT IDENTITY IS NOT ...THE LIGAND DENOTED AS PGT HAS BEEN CO-PURIFIED ALONG WITH THE PROTEIN AND ITS EXACT IDENTITY IS NOT KNOWN. PGT REPRESENTS A CLOSE MATCH.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 58.69 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 19% PEG8000, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0333
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2008
Radiation	Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0333 Å / Relative weight: 1
Reflection	Resolution: 2.91→20 Å / Num. all: 160125 / Num. obs: 160125 / % possible obs: 93.5 % / Redundancy: 2.1 % / R_merge(I) obs: 0.063 / Net I/σ(I): 18.2
Reflection shell	Resolution: 2.91→3 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.457 / Mean I/σ(I) obs: 1.8 / % possible all: 73

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASES		phasing
REFMAC	5.5.0110	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.91→20 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.902 / Cross valid method: THROUGHOUT / ESU R Free: 0.449 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27551	8030	5 %	RANDOM
R_work	0.2384	-	-	-
obs	0.24025	152067	92.5 %	-
all	-	152067	-	-

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 mean: 61.234 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7 Å²	0.98 Å²	-0.19 Å²
2-	-	-2.28 Å²	-1.92 Å²
3-	-	-	-4.95 Å²

Refinement step

Cycle: LAST / Resolution: 2.91→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	42570	0	1188	37	43795

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.021	44778
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	28025
X-RAY DIFFRACTION	r_angle_refined_deg	1.428	1.987	61233
X-RAY DIFFRACTION	r_angle_other_deg	4.496	3.001	68671
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.118	5	5646
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.014	25.609	1920
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.708	15	6575
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.57	15	102
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	7446
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	49695
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	8349
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	0.287	1.5	28259
X-RAY DIFFRACTION	r_mcbond_other	0	1.5	11397
X-RAY DIFFRACTION	r_mcangle_it	0.588	2	45054
X-RAY DIFFRACTION	r_scbond_it	1.159	3	16519
X-RAY DIFFRACTION	r_scangle_it	1.921	4.5	16179
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	B	1320	tight positional	0.04	0.05
1	1	F	1320	tight positional	0.04	0.05
1	1	J	1320	tight positional	0.03	0.05
1	1	N	1320	tight positional	0.04	0.05
1	1	A	1320	tight positional	0.04	0.05
1	1	E	1320	tight positional	0.04	0.05
1	1	I	1320	tight positional	0.04	0.05
1	1	M	1320	tight positional	0.04	0.05
2	2	C	1434	tight positional	0.04	0.05
2	2	D	1434	tight positional	0.04	0.05
2	2	H	1434	tight positional	0.04	0.05
2	2	K	1434	tight positional	0.04	0.05
2	2	L	1434	tight positional	0.04	0.05
2	2	O	1434	tight positional	0.04	0.05
2	2	P	1434	tight positional	0.04	0.05
2	2	G	1434	tight positional	0.04	0.05
3	3	B	2686	tight positional	0.04	0.05
3	3	A	2686	tight positional	0.04	0.05
3	3	E	2686	tight positional	0.03	0.05
3	3	I	2686	tight positional	0.03	0.05
3	3	M	2686	tight positional	0.04	0.05
3	3	F	2686	tight positional	0.03	0.05
3	3	J	2686	tight positional	0.03	0.05
3	3	N	2686	tight positional	0.04	0.05
4	4	B	326	tight positional	0.05	0.05
4	4	A	326	tight positional	0.05	0.05
4	4	I	326	tight positional	0.1	0.05
4	4	M	326	tight positional	0.04	0.05
4	4	E	326	tight positional	0.04	0.05
4	4	F	326	tight positional	0.04	0.05
4	4	J	326	tight positional	0.04	0.05
4	4	N	326	tight positional	0.04	0.05
5	5	B	214	tight positional	0.06	0.05
5	5	A	214	tight positional	0.1	0.05
5	5	E	214	tight positional	0.05	0.05
5	5	I	214	tight positional	0.13	0.05
5	5	M	214	tight positional	0.06	0.05
5	5	F	214	tight positional	0.05	0.05
5	5	J	214	tight positional	0.06	0.05
5	5	N	214	tight positional	0.05	0.05
6	6	D	76	tight positional	0.03	0.05
6	6	H	76	tight positional	0.02	0.05
6	6	L	76	tight positional	0.03	0.05
6	6	P	76	tight positional	0.02	0.05
7	7	B	98	tight positional	0.05	0.05
7	7	F	98	tight positional	0.04	0.05
7	7	J	98	tight positional	0.04	0.05
7	7	N	98	tight positional	0.05	0.05
7	7	A	98	tight positional	0.04	0.05
7	7	E	98	tight positional	0.03	0.05
7	7	I	98	tight positional	0.09	0.05
7	7	M	98	tight positional	0.04	0.05
8	8	B	796	tight positional	0.04	0.05
8	8	F	796	tight positional	0.03	0.05
8	8	J	796	tight positional	0.04	0.05
8	8	N	796	tight positional	0.04	0.05
8	8	A	796	tight positional	0.04	0.05
8	8	E	796	tight positional	0.03	0.05
8	8	M	796	tight positional	0.04	0.05
1	1	B	1320	tight thermal	0.09	0.5
1	1	F	1320	tight thermal	0.08	0.5
1	1	J	1320	tight thermal	0.07	0.5
1	1	N	1320	tight thermal	0.09	0.5
1	1	A	1320	tight thermal	0.1	0.5
1	1	E	1320	tight thermal	0.08	0.5
1	1	I	1320	tight thermal	0.08	0.5
1	1	M	1320	tight thermal	0.1	0.5
2	2	C	1434	tight thermal	0.09	0.5
2	2	D	1434	tight thermal	0.09	0.5
2	2	H	1434	tight thermal	0.08	0.5
2	2	K	1434	tight thermal	0.07	0.5
2	2	L	1434	tight thermal	0.08	0.5
2	2	O	1434	tight thermal	0.09	0.5
2	2	P	1434	tight thermal	0.09	0.5
2	2	G	1434	tight thermal	0.08	0.5
3	3	B	2686	tight thermal	0.09	0.5
3	3	A	2686	tight thermal	0.07	0.5
3	3	E	2686	tight thermal	0.06	0.5
3	3	I	2686	tight thermal	0.05	0.5
3	3	M	2686	tight thermal	0.07	0.5
3	3	F	2686	tight thermal	0.05	0.5
3	3	J	2686	tight thermal	0.06	0.5
3	3	N	2686	tight thermal	0.07	0.5
4	4	B	326	tight thermal	0.15	0.5
4	4	A	326	tight thermal	0.09	0.5
4	4	I	326	tight thermal	0.06	0.5
4	4	M	326	tight thermal	0.08	0.5
4	4	E	326	tight thermal	0.07	0.5
4	4	F	326	tight thermal	0.07	0.5
4	4	J	326	tight thermal	0.07	0.5
4	4	N	326	tight thermal	0.09	0.5
5	5	B	214	tight thermal	0.22	0.5
5	5	A	214	tight thermal	0.12	0.5
5	5	E	214	tight thermal	0.18	0.5
5	5	I	214	tight thermal	0.19	0.5
5	5	M	214	tight thermal	0.11	0.5
5	5	F	214	tight thermal	0.12	0.5
5	5	J	214	tight thermal	0.13	0.5
5	5	N	214	tight thermal	0.19	0.5
6	6	D	76	tight thermal	0.08	0.5
6	6	H	76	tight thermal	0.08	0.5
6	6	L	76	tight thermal	0.05	0.5
6	6	P	76	tight thermal	0.06	0.5
7	7	B	98	tight thermal	0.16	0.5
7	7	F	98	tight thermal	0.07	0.5
7	7	J	98	tight thermal	0.07	0.5
7	7	N	98	tight thermal	0.12	0.5
7	7	A	98	tight thermal	0.1	0.5
7	7	E	98	tight thermal	0.07	0.5
7	7	I	98	tight thermal	0.07	0.5
7	7	M	98	tight thermal	0.07	0.5
8	8	B	796	tight thermal	0.1	0.5
8	8	F	796	tight thermal	0.07	0.5
8	8	J	796	tight thermal	0.06	0.5
8	8	N	796	tight thermal	0.09	0.5
8	8	A	796	tight thermal	0.07	0.5
8	8	E	796	tight thermal	0.06	0.5
8	8	M	796	tight thermal	0.07	0.5

LS refinement shell

Resolution: 2.906→2.979 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.45	397	-
R_work	0.409	7121	-
obs	-	-	59.7 %

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	0.6186	-0.1836	0.1498	2.8955	-0.9283	0.3443	-0.0366	-0.0488	-0.1561	0.0888	0.1181	0.1491	0.0313	-0.1052	-0.0815	0.2276	0.006	0.076	0.3006	0.0817	0.229	5.174	-6.666	6.251
2	0.4508	-0.1904	0.0795	2.4013	0.0303	0.8623	-0.0322	-0.0828	0.0398	0.1866	0.1011	-0.1926	-0.0186	0.1443	-0.069	0.0289	0.0057	0.0231	0.2577	0.0609	0.1682	18.612	56.244	5.142
3	0.8744	-0.1295	0.2353	0.4148	0.4559	4.5417	0.2374	0.3048	-0.112	-0.3013	0.0339	0.1717	0.2933	-0.2599	-0.2713	0.3687	0.0586	-0.1095	0.5464	0.0646	0.4382	54.135	69.5	0.082
4	0.9189	0.0012	-0.1583	0.668	0.1858	2.8124	0.0369	-0.1326	-0.2569	0.2761	0.1123	-0.2207	0.6221	0.5225	-0.1491	0.3125	0.2166	-0.1188	0.4719	0.0228	0.5263	66.846	67.784	63.32
5	1.2956	0.5018	0.5485	2.0998	0.4976	4.0489	-0.0057	-0.3627	0.2922	0.6811	-0.0789	0.1048	-0.6321	-0.6189	0.0845	0.4927	0.0565	0.1898	0.5892	-0.0185	0.4641	52.306	-0.546	76.84
6	0.7571	-0.0663	-0.0196	0.8303	0.1541	2.1909	-0.0245	0.1678	0.2718	-0.1212	0.0228	-0.3412	-0.4721	0.3875	0.0016	0.331	-0.1752	0.2814	0.5397	0.0764	0.6743	70.724	-4.382	25.84
7	0.6885	-0.2512	0.0313	2.8693	-0.9826	0.5554	0.0612	0.0461	0.1078	-0.1471	0.0476	0.2975	-0.1524	-0.1061	-0.1089	0.2141	0.0466	0.0374	0.3285	0.0672	0.256	0.843	66.397	77.316
8	0.3484	0.0664	-0.1898	2.6841	0.0354	0.5774	-0.0815	0.0824	0.0078	-0.458	0.0594	-0.1923	0.0993	0.0995	0.0222	0.1849	0.044	0.1091	0.2843	0.0771	0.1753	17.218	4.188	79.315
9	2.2987	0.9439	-0.4619	3.7173	0.2695	2.9413	0.094	-0.1168	-0.0713	0.0783	0.0697	-0.699	0.3329	0.4937	-0.1638	0.2507	0.1634	-0.0157	0.2466	0.0289	0.2563	25.811	4.163	0.269
10	0.8586	0.4952	1.0545	6.6714	1.517	3.67	0.0483	-0.2152	-0.2399	-0.4484	-0.068	1.0642	-0.3355	-0.3969	0.0196	0.1152	0.0565	-0.0965	0.1774	0.1018	0.3301	-1.228	44.498	-0.423
11	3.71	-0.0644	0.9083	2.0281	-0.1298	2.5908	0.458	0.1589	0.0969	-0.3	-0.0028	-0.3974	0.1558	0.8021	-0.4553	0.1423	0.1096	0.1523	0.5734	-0.1125	0.4564	74.006	76.41	11.559
12	4.1036	-0.2245	0.4102	2.6544	0.1698	2.4683	0.0339	0.1259	-0.2708	0.2934	0.0842	-0.0219	0.1316	-0.3672	-0.1181	0.1949	0.1542	0.0521	0.4175	0.1141	0.2463	46.465	71.356	51.713
13	2.2549	0.7516	0.3604	5.3606	1.313	3.9185	0.2604	-0.3626	0.0244	0.8273	0.1012	-1.1731	0.2858	0.5163	-0.3617	0.4474	-0.0769	-0.1524	0.4933	0.0107	0.6352	73.146	-12.652	78.145
14	3.8118	1.1119	-0.386	1.9775	0.1868	1.8155	0.0916	-0.1035	0.3744	-0.499	-0.0457	0.0696	-0.3958	-0.2586	-0.0458	0.3637	-0.0713	0.1403	0.3769	0.063	0.3207	49.631	-9.278	35.195
15	1.4517	-1.1533	0.3855	3.6946	0.4253	3.9016	0.1251	0.1531	0.2006	-0.0302	-0.068	-0.6361	-0.3181	0.5499	-0.057	0.1622	-0.0595	0.0929	0.2729	0.1179	0.2623	21.534	56.874	84.522
16	1.2496	0.0564	-0.1769	5.9561	0.7579	3.8863	0.0195	0.1516	0.1985	-0.006	-0.1274	1.2611	0.3294	-0.395	0.1079	0.1557	-0.0259	0.0518	0.2124	0.0579	0.4044	-2.876	14.972	83.608

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	26 - 619
2	X-RAY DIFFRACTION	2	B	27 - 625
3	X-RAY DIFFRACTION	3	E	26 - 617
4	X-RAY DIFFRACTION	4	F	27 - 625
5	X-RAY DIFFRACTION	5	I	26 - 529
6	X-RAY DIFFRACTION	6	J	27 - 625
7	X-RAY DIFFRACTION	7	M	26 - 618
8	X-RAY DIFFRACTION	8	N	27 - 625
9	X-RAY DIFFRACTION	9	C	21 - 158
10	X-RAY DIFFRACTION	10	D	23 - 158
11	X-RAY DIFFRACTION	11	G	21 - 158
12	X-RAY DIFFRACTION	12	H	23 - 160
13	X-RAY DIFFRACTION	13	K	21 - 157
14	X-RAY DIFFRACTION	14	L	23 - 160
15	X-RAY DIFFRACTION	15	O	21 - 158
16	X-RAY DIFFRACTION	16	P	23 - 157

-
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://pdbjlvh1.pdbj.org/emnavi/covid19.php

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

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

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

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

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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 2 types, 16 molecules AEIMBFJNCDGHKLOP

-
Sugars , 2 types, 16 molecules

-
Non-polymers , 2 types, 41 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 2 types, 16 molecules AEIMBFJNCDGHKLOP

-Sugars , 2 types, 16 molecules

-Non-polymers , 2 types, 41 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 2 types, 16 molecules AEIMBFJNCDGHKLOP

-
Sugars , 2 types, 16 molecules

-
Non-polymers , 2 types, 41 molecules

-
Details

-
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