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- PDB-5b5m: Crystal structure of the Sr-substituted LH1-RC complex from Tch. ... -

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Basic information

Entry
Database: PDB / ID: 5b5m
TitleCrystal structure of the Sr-substituted LH1-RC complex from Tch. tepidum
Components
  • (Photosynthetic reaction center ...) x 4
  • LH1 alpha polypeptide
  • LH1 beta polypeptide
KeywordsPHOTOSYNTHESIS / Bacterial photosynthesis / Light-harvesting complex
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / iron ion binding ...organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE 8 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGW / PHOSPHATE ION / STRONTIUM ION ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE 8 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGW / PHOSPHATE ION / STRONTIUM ION / Ubiquinone-8 / Reaction center protein M chain / LH1 beta polypeptide / LH1 alpha polypeptide / Reaction center protein L chain / Photosynthetic reaction center cytochrome c subunit / Photosynthetic reaction center H subunit
Similarity search - Component
Biological speciesThermochromatium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWang-Otomo, Z.-Y. / Yu, L.-J.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Basis for the Unusual Qy Red-Shift and Enhanced Thermostability of the LH1 Complex from Thermochromatium tepidum.
Authors: Yu, L.J. / Kawakami, T. / Kimura, Y. / Wang-Otomo, Z.Y.
History
DepositionMay 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_conn.ptnr2_label_seq_id
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Category: entity_src_nat

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Photosynthetic reaction center cytochrome c subunit
L: Photosynthetic reaction center L subunit
M: Photosynthetic reaction center M subunit
H: Photosynthetic reaction center H subunit
A: LH1 alpha polypeptide
B: LH1 beta polypeptide
D: LH1 alpha polypeptide
E: LH1 beta polypeptide
F: LH1 alpha polypeptide
G: LH1 beta polypeptide
I: LH1 alpha polypeptide
J: LH1 beta polypeptide
K: LH1 alpha polypeptide
N: LH1 beta polypeptide
O: LH1 alpha polypeptide
P: LH1 beta polypeptide
Q: LH1 alpha polypeptide
R: LH1 beta polypeptide
S: LH1 alpha polypeptide
T: LH1 beta polypeptide
U: LH1 alpha polypeptide
V: LH1 beta polypeptide
W: LH1 alpha polypeptide
X: LH1 beta polypeptide
Y: LH1 alpha polypeptide
Z: LH1 beta polypeptide
1: LH1 alpha polypeptide
2: LH1 beta polypeptide
3: LH1 alpha polypeptide
4: LH1 beta polypeptide
5: LH1 alpha polypeptide
6: LH1 beta polypeptide
7: LH1 alpha polypeptide
8: LH1 beta polypeptide
9: LH1 alpha polypeptide
0: LH1 beta polypeptide
o: Photosynthetic reaction center cytochrome c subunit
x: Photosynthetic reaction center L subunit
y: Photosynthetic reaction center M subunit
t: Photosynthetic reaction center H subunit
m: LH1 alpha polypeptide
n: LH1 beta polypeptide
p: LH1 alpha polypeptide
q: LH1 beta polypeptide
r: LH1 alpha polypeptide
s: LH1 beta polypeptide
u: LH1 alpha polypeptide
v: LH1 beta polypeptide
w: LH1 alpha polypeptide
z: LH1 beta polypeptide
AA: LH1 alpha polypeptide
AB: LH1 beta polypeptide
AC: LH1 alpha polypeptide
AD: LH1 beta polypeptide
AE: LH1 alpha polypeptide
AF: LH1 beta polypeptide
AG: LH1 alpha polypeptide
AH: LH1 beta polypeptide
AI: LH1 alpha polypeptide
AJ: LH1 beta polypeptide
AK: LH1 alpha polypeptide
AL: LH1 beta polypeptide
d: LH1 alpha polypeptide
e: LH1 beta polypeptide
f: LH1 alpha polypeptide
g: LH1 beta polypeptide
h: LH1 alpha polypeptide
i: LH1 beta polypeptide
j: LH1 alpha polypeptide
k: LH1 beta polypeptide
l: LH1 alpha polypeptide
c: LH1 beta polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)780,577256
Polymers666,88672
Non-polymers113,691184
Water1086
1
C: Photosynthetic reaction center cytochrome c subunit
L: Photosynthetic reaction center L subunit
M: Photosynthetic reaction center M subunit
H: Photosynthetic reaction center H subunit
A: LH1 alpha polypeptide
B: LH1 beta polypeptide
D: LH1 alpha polypeptide
E: LH1 beta polypeptide
F: LH1 alpha polypeptide
G: LH1 beta polypeptide
I: LH1 alpha polypeptide
J: LH1 beta polypeptide
K: LH1 alpha polypeptide
N: LH1 beta polypeptide
O: LH1 alpha polypeptide
P: LH1 beta polypeptide
Q: LH1 alpha polypeptide
R: LH1 beta polypeptide
S: LH1 alpha polypeptide
T: LH1 beta polypeptide
U: LH1 alpha polypeptide
V: LH1 beta polypeptide
W: LH1 alpha polypeptide
X: LH1 beta polypeptide
Y: LH1 alpha polypeptide
Z: LH1 beta polypeptide
1: LH1 alpha polypeptide
2: LH1 beta polypeptide
3: LH1 alpha polypeptide
4: LH1 beta polypeptide
5: LH1 alpha polypeptide
6: LH1 beta polypeptide
7: LH1 alpha polypeptide
8: LH1 beta polypeptide
9: LH1 alpha polypeptide
0: LH1 beta polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)390,289128
Polymers333,44336
Non-polymers56,84692
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area211480 Å2
ΔGint-2386 kcal/mol
Surface area102440 Å2
MethodPISA
2
o: Photosynthetic reaction center cytochrome c subunit
x: Photosynthetic reaction center L subunit
y: Photosynthetic reaction center M subunit
t: Photosynthetic reaction center H subunit
m: LH1 alpha polypeptide
n: LH1 beta polypeptide
p: LH1 alpha polypeptide
q: LH1 beta polypeptide
r: LH1 alpha polypeptide
s: LH1 beta polypeptide
u: LH1 alpha polypeptide
v: LH1 beta polypeptide
w: LH1 alpha polypeptide
z: LH1 beta polypeptide
AA: LH1 alpha polypeptide
AB: LH1 beta polypeptide
AC: LH1 alpha polypeptide
AD: LH1 beta polypeptide
AE: LH1 alpha polypeptide
AF: LH1 beta polypeptide
AG: LH1 alpha polypeptide
AH: LH1 beta polypeptide
AI: LH1 alpha polypeptide
AJ: LH1 beta polypeptide
AK: LH1 alpha polypeptide
AL: LH1 beta polypeptide
d: LH1 alpha polypeptide
e: LH1 beta polypeptide
f: LH1 alpha polypeptide
g: LH1 beta polypeptide
h: LH1 alpha polypeptide
i: LH1 beta polypeptide
j: LH1 alpha polypeptide
k: LH1 beta polypeptide
l: LH1 alpha polypeptide
c: LH1 beta polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)390,289128
Polymers333,44336
Non-polymers56,84692
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area212550 Å2
ΔGint-2385 kcal/mol
Surface area102100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.888, 148.946, 210.226
Angle α, β, γ (deg.)90.00, 108.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Photosynthetic reaction center ... , 4 types, 8 molecules CoLxMyHt

#1: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 36630.484 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-333 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P5
#2: Protein Photosynthetic reaction center L subunit


Mass: 31520.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P3
#3: Protein Photosynthetic reaction center M subunit


Mass: 35975.992 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-319 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: A8ASG6
#4: Protein Photosynthetic reaction center H subunit


Mass: 28213.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P9

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Protein / Protein/peptide , 2 types, 64 molecules ADFIKOQSUWY13579mpruwAAACAEAGAIAKdfh...

#5: Protein ...
LH1 alpha polypeptide


Mass: 7034.442 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P2
#6: Protein/peptide ...
LH1 beta polypeptide


Mass: 5534.452 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P1

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Non-polymers , 12 types, 190 molecules

#7: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#8: Chemical...
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Sr
#9: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#10: Chemical
ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C55H76N4O6
#11: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C49H74O4
#12: Chemical
ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: C37H74NO8P / Comment: phospholipid*YM
#13: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe
#14: Chemical ChemComp-MQ8 / MENAQUINONE 8 / 2-METHYL-3-(3,7,11,15,19,23,27,31-OCTAMETHYL-DOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL)-[1,4]NAPTHOQUINONE


Mass: 717.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C51H72O2
#15: Chemical...
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: C42H60O2
#16: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: PO4
#17: Chemical ChemComp-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL


Mass: 749.007 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C40H77O10P / Comment: phospholipid*YM
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3000, strontium chloride, decylphosphocholine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→48.182 Å / Num. obs: 142696 / % possible obs: 98 % / Redundancy: 6.4 % / Net I/σ(I): 20.4
Reflection shellResolution: 3.3→3.36 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WMM

3wmm


Resolution: 3.3→48.182 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3093 7021 4.92 %
Rwork0.2713 --
obs0.2732 142691 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→48.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44418 0 7457 6 51881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03553919
X-RAY DIFFRACTIONf_angle_d2.26174475
X-RAY DIFFRACTIONf_dihedral_angle_d18.23418873
X-RAY DIFFRACTIONf_chiral_restr0.1597670
X-RAY DIFFRACTIONf_plane_restr0.0128810
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.33750.46042180.41684457X-RAY DIFFRACTION97
3.3375-3.37670.42592800.40464488X-RAY DIFFRACTION98
3.3767-3.41790.45142160.39314474X-RAY DIFFRACTION98
3.4179-3.46120.42162720.38534507X-RAY DIFFRACTION99
3.4612-3.50670.41182250.36244535X-RAY DIFFRACTION99
3.5067-3.55470.39422270.35724518X-RAY DIFFRACTION99
3.5547-3.60550.36812360.33864483X-RAY DIFFRACTION99
3.6055-3.65930.34492160.32474569X-RAY DIFFRACTION99
3.6593-3.71640.37892220.32284543X-RAY DIFFRACTION99
3.7164-3.77740.34582170.32074561X-RAY DIFFRACTION99
3.7774-3.84250.36082490.30524554X-RAY DIFFRACTION99
3.8425-3.91230.31532160.28914554X-RAY DIFFRACTION99
3.9123-3.98750.33582260.28014506X-RAY DIFFRACTION99
3.9875-4.06890.3162470.26454539X-RAY DIFFRACTION99
4.0689-4.15730.29222050.24844569X-RAY DIFFRACTION99
4.1573-4.25390.29172160.23784601X-RAY DIFFRACTION99
4.2539-4.36030.30782340.23564568X-RAY DIFFRACTION99
4.3603-4.47810.30072630.24484530X-RAY DIFFRACTION99
4.4781-4.60970.2732160.23274573X-RAY DIFFRACTION99
4.6097-4.75840.27762320.22614550X-RAY DIFFRACTION99
4.7584-4.92830.27132110.22024589X-RAY DIFFRACTION99
4.9283-5.12540.24222310.22094594X-RAY DIFFRACTION99
5.1254-5.35840.27152300.23094575X-RAY DIFFRACTION99
5.3584-5.64050.30652310.23254556X-RAY DIFFRACTION99
5.6405-5.99330.27742570.23394620X-RAY DIFFRACTION100
5.9933-6.4550.30792530.2384590X-RAY DIFFRACTION100
6.455-7.10280.29562550.24074601X-RAY DIFFRACTION99
7.1028-8.12630.2732400.24924574X-RAY DIFFRACTION99
8.1263-10.22220.25942810.23974522X-RAY DIFFRACTION98
10.2222-48.18740.33351990.31153770X-RAY DIFFRACTION79
Refinement TLS params.Method: refined / Origin x: -106.4617 Å / Origin y: -13.4516 Å / Origin z: 448.4792 Å
111213212223313233
T0.4305 Å2-0.1822 Å2-0.3175 Å2-0.2349 Å2-0.0855 Å2--1.039 Å2
L1.4826 °20.0243 °2-2.4587 °2-0.4723 °2-0.0208 °2--6.334 °2
S0.0339 Å °-0.2166 Å °-0.0539 Å °0.0743 Å °-0.1089 Å °-0.017 Å °-0.0503 Å °0.238 Å °-0.0357 Å °
Refinement TLS groupSelection details: all

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