[English] 日本語
Yorodumi
- PDB-3d32: Complex of GABA(A) receptor-associated protein (GABARAP) with a s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d32
TitleComplex of GABA(A) receptor-associated protein (GABARAP) with a synthetic peptide
Components
  • Gamma-aminobutyric acid receptor-associated protein
  • K1 peptide
KeywordsTRANSPORT PROTEIN / alpha-beta / beta-grasp fold / Cytoskeleton / Golgi apparatus / Membrane / Microtubule / Transport
Function / homology
Function and homology information


positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Macroautophagy / beta-tubulin binding ...positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Macroautophagy / beta-tubulin binding / autophagosome membrane / extrinsic apoptotic signaling pathway via death domain receptors / axoneme / autophagosome assembly / autophagosome maturation / smooth endoplasmic reticulum / protein targeting / mitophagy / sperm midpiece / autophagosome / GABA-ergic synapse / microtubule cytoskeleton organization / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / microtubule binding / cytoplasmic vesicle / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / plasma membrane / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsWeiergraeber, O.H. / Stangler, T. / Willbold, D.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Ligand Binding Mode of GABA(A) Receptor-Associated Protein.
Authors: Weiergraber, O.H. / Stangler, T. / Thielmann, Y. / Mohrluder, J. / Wiesehan, K. / Willbold, D.
History
DepositionMay 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Mar 4, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.details
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein
B: Gamma-aminobutyric acid receptor-associated protein
C: K1 peptide
D: K1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,45613
Polymers31,1504
Non-polymers3079
Water5,423301
1
A: Gamma-aminobutyric acid receptor-associated protein
C: K1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7407
Polymers15,5752
Non-polymers1655
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-57 kcal/mol
Surface area7150 Å2
MethodPISA
2
B: Gamma-aminobutyric acid receptor-associated protein
D: K1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7176
Polymers15,5752
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-47 kcal/mol
Surface area7390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.287, 35.415, 58.209
Angle α, β, γ (deg.)90.000, 100.590, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein / GABA(A) receptor-associated protein / MM46


Mass: 14086.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Product contains an N-terminal cloning artifact (glycine-serine) preceding the sequence of native GABARAP.
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O95166
#2: Protein/peptide K1 peptide


Mass: 1488.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 285 K / Method: vapor diffusion / pH: 5.9
Details: 30 % (w/v) PEG3350 800 mM NaCl 50 mM MES, pH 5.9, VAPOR DIFFUSION, temperature 285K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2006 / Details: monochromators, mirrors
RadiationMonochromator: diamond, germanium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.3→63.5 Å / Num. all: 60022 / Num. obs: 60022 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 16.3
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.7 / Num. unique all: 8554 / Rsym value: 0.32 / % possible all: 92.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å25.83 Å
Translation2 Å25.83 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.2data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GNU

1gnu


Resolution: 1.3→27.17 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.604 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic + tls / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.056 / Stereochemistry target values: Engh & Huber
Details: The B factor column contains residual B values after TLS refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 3070 5.1 %SHELLS
Rwork0.177 ---
all0.178 60022 --
obs0.178 60022 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.922 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20.19 Å2
2--0.65 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 11 301 2472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222372
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9483229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06122.941119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96415403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.171517
X-RAY DIFFRACTIONr_chiral_restr0.0910.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211879
X-RAY DIFFRACTIONr_mcbond_it0.611.51395
X-RAY DIFFRACTIONr_mcangle_it1.01322283
X-RAY DIFFRACTIONr_scbond_it1.6393977
X-RAY DIFFRACTIONr_scangle_it2.2444.5946
LS refinement shellHighest resolution: 1.3 Å / Num. reflection Rwork: 4311 / Num. reflection all: 4312 / Total num. of bins used: 20
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
111.2651.9872-1.00945.5784-1.93731.8754-0.0205-0.9284-0.32040.7824-0.02240.26280.05650.23160.04280.05050.0260.03020.06910.04470.063458.00910.60819.223
212.69233.50951.27131.5977-1.774311.5619-0.11270.1224-1.074-0.27920.08-0.47450.54630.23090.0327-0.00520.01750.02350.0364-0.03210.140261.5310.93210.721
37.96540.3681-0.56736.5410.95420.1877-0.00670.5386-0.03180.004-0.0455-0.18960.0410.00250.0522-0.00840.0104-0.01860.1281-0.01390.003166.56918.0468.514
48.303-3.51181.53944.4923-1.75256.5930.08320.55150.3889-0.1475-0.08-0.103-0.08920.2966-0.0032-0.0026-0.0218-0.00690.10650.03470.033163.32824.1976.723
59.79510.1568-3.078412.23113.02299.41080.17710.14470.270.0421-0.1925-0.1493-0.15530.32710.01540.0374-0.0188-0.02190.08690.03670.04557.36828.1345.887
68.07162.9672-3.78493.4197-3.92755.24490.14110.43180.3441-0.1289-0.02270.1207-0.4530.0499-0.11850.0790.0014-0.00420.0040.0150.030151.11129.3666.244
72.3691.4528-1.96835.3657-3.09223.3924-0.1893-0.0068-0.106-0.02070.069-0.01550.1801-0.01030.12020.02910.0020.00030.0411-0.00720.048752.29214.40714.696
811.3771.03233.774610.2022-0.56968.3104-0.0838-0.3967-0.86650.5879-0.031-0.24510.85680.34760.11470.16790.04050.0774-0.01780.01730.140148.0642.67420.221
94.32992.861-2.843910.9449-0.79682.0098-0.27590.1787-0.2519-0.20520.1338-0.05460.2602-0.00590.14210.0594-0.00190.00130.0256-0.01940.051250.23912.4098.241
104.4014-1.1518-3.46083.36362.24114.79430.04370.14430.1321-0.1540.0310.0086-0.2032-0.1546-0.07480.04460.0043-0.01470.0410.00820.04645.87826.07111.99
111.57920.8336-0.41062.63090.43471.537-0.03770.0018-0.0211-0.0926-0.04710.02960.0572-0.07910.08470.03020.0048-0.01030.0432-0.00310.029939.67617.89317.28
124.32851.974-4.10115.0047-7.019810.3461-0.53390.3555-0.2865-0.31850.2144-0.02280.7849-0.66360.31950.0846-0.06720.02860.0428-0.03650.017837.8039.44212.603
131.32660.74260.65622.28310.02622.34680.0806-0.0284-0.1317-0.0843-0.09580.15430.2344-0.16620.01520.0497-0.01260.00540.0268-0.00940.034637.2979.13423.58
147.16410.66961.44634.87812.96187.0084-0.1517-0.3848-0.23840.15170.2116-0.28610.04430.6546-0.05990.01430.0199-0.00550.10530.010.021451.93716.35324.562
158.7974-5.80042.89235.6462-1.73773.0492-0.0185-0.18630.1820.1132-0.0092-0.1087-0.03290.07250.02770.0435-0.0023-0.00380.0673-0.00440.016345.73121.37926.471
169.29831.50170.33062.0297-2.04633.94160.1953-0.2330.38230.040.0121-0.0001-0.20080.1117-0.20740.0289-0.0061-0.00780.0315-0.01850.041348.15326.98319.905
1710.1583-2.9155-1.75795.50440.214810.409-0.1009-0.68640.58390.30150.201-0.0977-0.4256-0.1257-0.10010.0243-0.015-0.02270.0873-0.03090.062555.30427.45720.399
187.2150.0741-0.28222.30690.73012.1447-0.0521-0.19650.24120.02330.067-0.10690.08670.2415-0.01490.003-0.0032-0.00830.0731-0.01310.035860.56822.76915.352
194.94523.8612-2.19863.5725-2.15521.3223-0.0482-0.1209-0.08760.0663-0.03770.05530.03120.24990.08590.0383-0.00130.02390.0363-0.00370.048251.21613.51718.942
209.92520.17432.59058.17252.103410.496-0.1682-0.4013-0.04710.5340.2727-0.77150.31090.5438-0.10440.04860.04970.022-0.00650.03040.088548.3658.2428.677
215.831-0.40923.03034.28370.49688.3604-0.0385-0.6248-0.02490.3570.0824-0.01670.1721-0.4057-0.0440.0184-0.01540.00020.0547-0.01030.028223.09915.39244.248
223.36670.5954-1.100610.0394-0.70073.3885-0.0649-0.13420.2283-0.12180.05040.2512-0.2006-0.09970.01450.0296-0.0105-0.02380.0464-0.00020.05518.9812.49838.007
235.9331-0.0534-1.57591.3123-0.13492.941-0.08030.3594-0.0412-0.09560.0586-0.1318-0.0679-0.04950.02160.0431-0.03230.00860.0395-0.01240.034223.5045.49434.154
2412.7080.2157-1.94532.7712-1.77981.4002-0.2312-0.1005-0.3807-0.1269-0.01180.04440.2029-0.00920.2430.072-0.01070.04220.0316-0.03510.078132.9091.51132.692
251.6602-1.6471-1.98093.46132.78133.6456-0.1164-0.0871-0.04750.02520.0544-0.01760.21160.1250.0620.0613-0.00060.00630.02960.00280.039835.7619.89337.546
260.9133-3.9975-1.788717.66967.03467.14710.0703-0.11120.21150.108-0.16860.1726-0.7398-0.62790.09830.11180.0518-0.02450.0457-0.07220.06827.80928.21847.285
270.8542-2.6794-1.695412.50058.027111.5417-0.07650.03480.3444-0.2194-0.09280.0933-0.4769-0.1750.16930.04740.01490.00260.03830.00260.07732.45125.36237.485
283.2218-1.7636-1.10964.96920.40910.66390.03920.08120.0013-0.1169-0.07160.104-0.0613-0.07040.03240.0490.00360.00280.0252-0.00510.024334.13814.92936.08
292.56752.38562.84682.80861.31077.12960.018-0.0995-0.3531-0.0468-0.1038-0.23620.23510.30770.0859-0.00040.01840.00020.0610.03080.069544.57410.17241.829
302.3741-0.3721.00851.82560.00230.80460.0377-0.04530.0443-0.0348-0.119-0.0285-0.07040.06960.08130.0133-0.0127-0.01430.07830.01320.020543.41220.4243.852
312.9123.48511.16815.4384.16686.5190.0295-0.10610.328-0.1219-0.30030.3067-0.19870.00150.27080.0469-0.0073-0.02820.02420.00560.054141.93827.21940.721
329.96691.4747-4.19384.49524.10418.64990.4015-1.38870.19040.3524-0.1485-0.2115-0.4940.7553-0.25310.1133-0.0599-0.00680.12230.00060.117543.18432.17845.236
336.00053.6322-3.80775.7143-1.13527.45180.3823-0.41530.29780.321-0.22630.013-0.49960.598-0.1560.0635-0.056-0.01780.0896-0.02430.014437.08923.53450.332
3415.22155.19340.51015.41960.83637.73470.046-0.3411-0.19820.051-0.15690.10330.3107-0.24930.11080.0832-0.0179-0.00290.0530.0090.011633.04914.48353.739
354.06591.46122.17333.89270.84032.80460.0197-0.3305-0.28280.1823-0.0386-0.16910.05940.07910.0190.0059-0.0059-0.01180.08240.05140.026943.57612.49149.857
3611.59372.83230.66257.3962.37333.68830.0978-0.296-0.57440.408-0.0671-0.30220.26170.1316-0.03060.0616-0.00370.00170.04340.02050.072837.6345.38746.655
3716.5782-0.71391.8444.34070.15056.7525-0.1074-0.2824-0.11090.15350.008-0.11180.0090.01830.09940.0829-0.01650.00810.05020.01650.059730.4595.75647.427
386.45174.3087-1.88065.206-0.23852.6072-0.0166-0.1011-0.3712-0.0928-0.0421-0.1460.1431-0.2140.05870.0578-0.00740.00030.0198-0.0040.050928.1165.68340.994
391.61392.67930.40638.00461.70551.19780.074-0.07380.05540.1041-0.1496-0.04120.0229-0.0540.07560.0404-0.0048-0.0080.0472-0.00860.028531.40118.59345.691
405.51561.9338-2.33265.9108-1.318912.5678-0.0695-0.19520.3010.06810.18980.535-0.4009-0.9251-0.12030.0684-0.0076-0.00270.089-0.00960.012230.59624.86554.362
413.2312-2.6284-1.60375.76524.06933.5463-0.00130.22310.0314-0.102-0.10170.0849-0.0643-0.20470.10310.02550.0102-0.00710.03470.01040.024238.56823.05510.639
4213.1360.1549-0.86070.3528-0.18514.4972-0.06660.4385-0.0488-0.01770.0351-0.0740.04840.07550.03140.0604-0.0056-0.01520.0492-0.00670.043546.37420.5834.724
433.6693-0.92631.59831.631-1.26742.1950.02250.0697-0.20220.0747-0.04290.0074-0.0820.30.02040.0209-0.0058-0.01050.06220.00040.019347.32316.56937.875
444.44632.8570.21192.07590.6991.3297-0.02350.046-0.04570.05660.0030.0250.05950.02780.02050.04880.00110.00720.0517-0.00160.027939.21814.60631.844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 61 - 6
2X-RAY DIFFRACTION2AA7 - 117 - 11
3X-RAY DIFFRACTION3AA12 - 1612 - 16
4X-RAY DIFFRACTION4AA17 - 2117 - 21
5X-RAY DIFFRACTION5AA22 - 2522 - 25
6X-RAY DIFFRACTION6AA26 - 3126 - 31
7X-RAY DIFFRACTION7AA32 - 3832 - 38
8X-RAY DIFFRACTION8AA39 - 4539 - 45
9X-RAY DIFFRACTION9AA46 - 5146 - 51
10X-RAY DIFFRACTION10AA52 - 5752 - 57
11X-RAY DIFFRACTION11AA58 - 6758 - 67
12X-RAY DIFFRACTION12AA68 - 7268 - 72
13X-RAY DIFFRACTION13AA73 - 7973 - 79
14X-RAY DIFFRACTION14AA80 - 8480 - 84
15X-RAY DIFFRACTION15AA85 - 9085 - 90
16X-RAY DIFFRACTION16AA91 - 9691 - 96
17X-RAY DIFFRACTION17AA97 - 10097 - 100
18X-RAY DIFFRACTION18AA101 - 107101 - 107
19X-RAY DIFFRACTION19AA108 - 112108 - 112
20X-RAY DIFFRACTION20AA113 - 118113 - 118
21X-RAY DIFFRACTION21BB3 - 83 - 8
22X-RAY DIFFRACTION22BB9 - 139 - 13
23X-RAY DIFFRACTION23BB14 - 2014 - 20
24X-RAY DIFFRACTION24BB21 - 2621 - 26
25X-RAY DIFFRACTION25BB27 - 3627 - 36
26X-RAY DIFFRACTION26BB37 - 4237 - 42
27X-RAY DIFFRACTION27BB43 - 4843 - 48
28X-RAY DIFFRACTION28BB49 - 5349 - 53
29X-RAY DIFFRACTION29BB54 - 5854 - 58
30X-RAY DIFFRACTION30BB59 - 6659 - 66
31X-RAY DIFFRACTION31BB67 - 7067 - 70
32X-RAY DIFFRACTION32BB71 - 7571 - 75
33X-RAY DIFFRACTION33BB76 - 8176 - 81
34X-RAY DIFFRACTION34BB82 - 8782 - 87
35X-RAY DIFFRACTION35BB88 - 9388 - 93
36X-RAY DIFFRACTION36BB94 - 9894 - 98
37X-RAY DIFFRACTION37BB99 - 10299 - 102
38X-RAY DIFFRACTION38BB103 - 107103 - 107
39X-RAY DIFFRACTION39BB108 - 112108 - 112
40X-RAY DIFFRACTION40BB113 - 118113 - 118
41X-RAY DIFFRACTION41CC1 - 61 - 6
42X-RAY DIFFRACTION42CC7 - 127 - 12
43X-RAY DIFFRACTION43DD1 - 61 - 6
44X-RAY DIFFRACTION44DD7 - 127 - 12

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more