[English] 日本語
Yorodumi
- PDB-2hrt: Asymmetric structure of trimeric AcrB from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hrt
TitleAsymmetric structure of trimeric AcrB from Escherichia coli
ComponentsAcriflavine resistance protein B
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / AcrB / multidrug efflux pump / RND / antibiotic resistance / AcrA / TolC / proton-coupled exchanger
Function / homology
Function and homology information


xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / outer membrane-bounded periplasmic space / identical protein binding / membrane / plasma membrane
Similarity search - Function
Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains ...Multidrug efflux transporter AcrB transmembrane fold / Multidrug efflux transporter AcrB transmembrane domain / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains / Multidrug efflux transporter AcrB pore domain / Multidrug efflux transporter AcrB pore domain like / Multidrug efflux transporter AcrB pore domain / Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Multidrug efflux pump subunit AcrB
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSeeger, M.A. / Schiefner, A. / Eicher, T. / Verrey, F. / Diederichs, K. / Pos, K.M.
CitationJournal: Science / Year: 2006
Title: Structural Asymmetry of AcrB Trimer Suggests a Peristaltic Pump Mechanism.
Authors: Seeger, M.A. / Schiefner, A. / Eicher, T. / Verrey, F. / Diederichs, K. / Pos, K.M.
History
DepositionJul 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acriflavine resistance protein B
B: Acriflavine resistance protein B
C: Acriflavine resistance protein B
D: Acriflavine resistance protein B
E: Acriflavine resistance protein B
F: Acriflavine resistance protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)689,17410
Polymers688,4186
Non-polymers7564
Water00
1
A: Acriflavine resistance protein B
B: Acriflavine resistance protein B
C: Acriflavine resistance protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,5875
Polymers344,2093
Non-polymers3782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19650 Å2
ΔGint-86 kcal/mol
Surface area114970 Å2
MethodPISA
2
D: Acriflavine resistance protein B
E: Acriflavine resistance protein B
F: Acriflavine resistance protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,5875
Polymers344,2093
Non-polymers3782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19740 Å2
ΔGint-83 kcal/mol
Surface area115090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.330, 134.870, 140.840
Angle α, β, γ (deg.)103.90, 94.64, 90.11
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a trimer. There are 2 biological units (trimers) in the asymmetric unit (chains A, B, C and chains D, E, F)

-
Components

#1: Protein
Acriflavine resistance protein B


Mass: 114736.289 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: acrB, acrE / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P31224
#2: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 290 K / pH: 4.6
Details: 5 % polyethylene glycol 400, 16-22 % polyethylene glycol 300, 8-11 % glycerol, 70 mM Nacitrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 4.60

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9737
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 3→29.8 Å / Num. obs: 181133 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 8.4
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

-
Phasing

Phasing MRRfactor: 0.368 / Cor.coef. Fo:Fc: 0.671
Highest resolutionLowest resolution
Rotation5 Å29.8 Å
Translation5 Å29.8 Å

-
Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IWG
Resolution: 3→29.8 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.879 / SU B: 48.918 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 9081 5 %RANDOM
Rwork0.231 ---
obs0.234 181137 99.9 %-
all-172056 --
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: 51.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0.01 Å2-0.19 Å2
2---0.08 Å20.08 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 3→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47046 0 52 0 47098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02247994
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.96865180
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.09256186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53524.5371878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.001158064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.81815222
X-RAY DIFFRACTIONr_chiral_restr0.070.27672
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0235610
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.223793
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.233666
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.21300
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1971.531455
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.354249508
X-RAY DIFFRACTIONr_scbond_it0.432318540
X-RAY DIFFRACTIONr_scangle_it0.7444.515672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 683 -
Rwork0.332 12568 -
obs--99.81 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.21380.0786-1.09451.66210.39952.3050.0027-0.60920.08750.21290.08640.183-0.1671-0.204-0.08910.08410.0725-0.02860.2445-0.0763-0.28011.2098.219736.736
23.6291.0434-2.92525.5545-0.56916.42030.16270.14680.1896-0.0594-0.0208-0.1918-0.217-0.1831-0.1419-0.57160.0265-0.0673-0.60540.0344-0.461814.825510.9212-12.1504
33.3522-1.0319-1.53353.66790.3964.11780.1138-0.6531-0.06370.25330.0064-0.6917-0.42560.5507-0.1202-0.3443-0.0062-0.0902-0.3227-0.0235-0.278332.18330.73694.566
41.70050.65820.30322.67571.48991.31150.06770.1912-0.4256-0.64450.0211-1.0984-0.16630.2761-0.0888-0.27970.10680.1515-0.4026-0.0337-0.008140.4093-10.2217-25.4578
53.0020.4699-2.81154.73350.125612.81870.3253-0.87530.83130.2167-0.1612-0.0982-1.32020.0938-0.16410.1771-0.24190.0217-0.0273-0.17310.063635.448620.55379.8276
64.5690.15220.07465.00364.16164.20640.2767-0.6341.00710.2794-0.07480.0669-0.742-0.0815-0.2019-0.2102-0.05880.2039-0.4727-0.07940.169616.637334.0429-5.1759
72.55060.4045-0.744.2024-1.77112.83290.02480.50630.1084-0.6403-0.0604-0.47660.08740.24270.0356-0.3289-0.01270.2113-0.3624-0.0075-0.089639.009711.3098-27.6891
82.2166-0.0028-0.32270.86350.49652.30050.0209-0.64670.67260.3963-0.1111-0.1802-0.7194-0.1210.09020.48710.09160.03030.2529-0.3710.0967-0.868527.878639.2573
91.6375-0.1039-1.63391.00780.01192.961-0.0686-0.2015-0.3980.2606-0.04930.25890.4204-0.62560.11790.0362-0.17760.02170.29910.3046-0.1404-19.4834-23.406222.0462
106.6711-1.2596-5.12763.03761.83745.46860.05990.256-0.4395-0.1793-0.28220.10770.1341-0.34550.2223-0.45490.0356-0.0695-0.5780.0508-0.37916.4465-12.106-10.0524
114.2643-2.1121-4.2811.10571.8775.2913-0.32340.3069-0.7649-0.0521-0.16550.20780.2127-0.37350.4888-0.1324-0.115-0.0457-0.15570.04770.0848-4.5606-28.4917-19.1394
121.3449-0.97051.44255.2228-1.55382.1730.34821.0838-0.4821-1.0914-0.4464-0.05190.29250.060.09820.01370.07320.02210.0967-0.0407-0.379711.5135-13.8566-44.6741
135.0846-0.0727-2.98452.9845-1.82876.0462-0.1406-0.5943-0.88110.71740.0916-0.28940.20320.06260.0490.1064-0.0450.1055-0.26020.07760.28037.5485-43.4597-8.5247
143.94610.1811-0.20046.0304-2.45926.3302-0.1357-0.9017-0.55080.5816-0.0437-0.2370.72770.00970.1795-0.18390.1826-0.0495-0.38730.2164-0.054727.4214-27.62085.1131
154.2303-2.21160.11341.6079-0.28021.63290.09290.79560.0017-0.7653-0.2255-0.49590.05860.03280.1325-0.1871-0.01270.1439-0.3342-0.1084-0.100628.1015-22.8372-33.6634
160.9019-0.1124-0.3951.54190.74942.7433-0.1363-0.4332-0.55280.49330.0763-0.13540.7815-0.09740.060.5211-0.00970.01080.25460.41690.0017-7.0846-32.000734.7545
173.29170.2985-0.07821.94280.20362.16530.1348-0.83330.36280.442-0.04680.4772-0.236-0.6137-0.088-0.22630.20090.03870.25670.0319-0.0832-31.477516.631314.86
181.9968-1.2071-0.90961.49041.278814.13110.11550.3945-0.1003-0.33380.0337-0.27760.37760.0775-0.1492-0.4198-0.0494-0.1159-0.34410.0464-0.2855-2.3376-3.8452-20.1893
195.79231.5627-2.14072.8544-0.88952.23390.17280.42150.8661-0.26640.03770.1556-0.4566-0.3169-0.2105-0.24570.2466-0.0404-0.32910.2443-0.1635-4.312224.1242-21.6378
203.07070.92581.47851.53250.26153.31320.0681.01480.5181-0.70340.1361-0.3093-0.27460.3441-0.2041-0.05320.01440.2518-0.24320.1402-0.15723.468718.2826-38.2995
215.3825-1.9541-2.7964.28182.88258.3910.06120.44360.3114-0.69780.08310.7173-0.2633-0.7375-0.1444-0.20650.2061-0.22380.08340.3891-0.0133-22.720218.9082-30.1102
226.25980.272-1.35843.2003-1.12124.45880.09580.5417-0.4313-0.3463-0.25480.50120.1236-0.91140.159-0.3419-0.0224-0.31590.17560.0705-0.3069-24.7734-3.8191-28.1655
231.1631-0.1259-0.19750.62970.04773.32770.11430.9902-0.0262-0.62830.1467-0.1412-0.1362-0.1453-0.26110.0850.10550.05770.15230.1329-0.39848.67685.5297-47.7666
243.7081-0.2891-1.29761.47610.22992.84220.1331-0.4061-0.09820.3846-0.21480.77290.0036-0.91030.0816-0.27430.03290.010.52670.1160.0724-46.3174.72028.3393
252.2356-0.1923-1.05541.48160.11792.1482-0.04510.64880.2779-0.49070.0838-0.1673-0.35570.2677-0.03880.2496-0.0803-0.02960.38070.1966-0.0805-52.745775.5754-77.9152
263.1127-1.4396-3.25484.79241.27826.47020.1838-0.11510.27220.02820.05510.2454-0.28140.1816-0.2389-0.5571-0.048-0.0564-0.5538-0.0201-0.4007-66.189778.4608-28.9902
274.67222.0167-0.80644.3817-0.31083.15310.04410.61790.1379-0.37340.04530.5535-0.3477-0.6228-0.0894-0.29960.0465-0.098-0.26840.1015-0.3389-83.494967.9552-45.5651
281.191-1.25510.42973.8981-1.80662.2420.1431-0.094-0.31450.576-0.15340.7424-0.0633-0.42250.0103-0.2365-0.19560.157-0.39730.0269-0.038-91.465457.1125-15.4351
293.9671-0.1172-3.26872.76020.1614.19430.43210.74960.9106-0.2481-0.14940.2428-1.5783-0.1424-0.28270.26750.2545-0.0533-0.09760.15980.2629-87.017187.6948-50.944
303.97160.30610.28416.3112-3.81484.41820.33920.78570.9409-0.3102-0.1448-0.0346-0.88270.115-0.1944-0.1540.05230.2629-0.40670.11840.2596-68.3047101.5099-36.1098
312.1605-0.755-0.54945.16192.76432.65360.1201-0.44870.19590.395-0.2030.3590.1463-0.47840.0829-0.3738-0.02710.2178-0.321-0.0109-0.0418-90.31278.6742-13.3521
321.36590.2494-0.61740.9351-0.2281.36660.09570.64710.6941-0.5281-0.04320.2239-0.6377-0.0242-0.05250.6135-0.04780.00730.43310.48810.4125-50.91295.2391-80.575
332.09860.1624-2.28031.54920.20512.8817-0.06010.215-0.3695-0.22370.0076-0.24020.22590.29710.0525-0.06560.08830.01370.1266-0.1862-0.2547-31.618744.2995-63.1044
345.48831.6435-4.12422.9875-1.17195.48610.0482-0.2475-0.41970.1853-0.2667-0.090.25470.42410.2185-0.4270.0015-0.0559-0.5488-0.0034-0.3919-67.546255.4019-30.9292
354.25781.9953-4.31952.0101-0.84277.4056-0.3706-0.5094-0.7360.1406-0.0357-0.22730.64970.82530.40640.12880.2715-0.0108-0.11750.1061-0.1355-46.308539.3292-21.8233
362.05021.29610.4494.74151.12941.51380.3478-1.2481-0.38540.9632-0.4047-0.14240.24280.18670.05690.10270.0153-0.08370.16260.0717-0.4207-62.448653.95363.6822
374.3250.2311-3.26423.72921.43576.966-0.24510.4412-0.8105-0.37430.11840.35550.56230.21920.12680.42060.14110.1347-0.22440.04880.0932-58.283324.1452-32.2874
382.7990.3728-0.94425.49313.31126.7053-0.12690.6807-0.4302-0.4499-0.00680.25220.76320.02960.1337-0.0791-0.1841-0.0027-0.411-0.1231-0.1599-78.399239.6526-45.9451
393.19681.53520.61610.76010.09561.87260.0973-0.63360.02950.6117-0.14260.35210.1860.01770.0453-0.08260.00020.1473-0.32550.1042-0.135-78.974744.7009-7.1989
402.3258-0.3509-0.76672.1549-0.36032.6042-0.12670.7716-0.4795-0.43530.0320.10530.5585-0.23730.09470.3301-0.09610.08670.2804-0.3605-0.1305-43.967435.4704-75.7029
412.6296-0.1061-0.93331.5458-0.3912.12930.14360.43920.5137-0.42390.126-0.349-0.26380.2741-0.2696-0.1405-0.26920.08670.1438-0.15990.0447-20.070684.5252-56.234
422.81580.4812-1.09182.0287-1.288111.40790.0492-0.4985-0.16780.32260.11350.30850.47310.1991-0.1627-0.37490.0804-0.1394-0.2197-0.0241-0.2524-48.819363.9546-20.9269
436.0413-1.6341-1.88382.2120.69433.41160.2425-0.47390.84470.33680.03270.0364-0.5260.5211-0.2752-0.2503-0.28990.0535-0.2427-0.3305-0.0196-47.170691.9548-19.6718
443.5206-0.52250.71911.54440.02752.723-0.0171-0.98140.42220.61810.21360.2102-0.4464-0.1174-0.1965-0.1030.00780.2233-0.1941-0.2138-0.1375-74.810785.9041-2.854
454.15311.5677-2.26024.7284-2.22468.72080.2901-0.50470.16060.627-0.06-0.7066-0.30241.0997-0.23-0.1768-0.215-0.14170.2846-0.4547-0.0076-28.66787.0158-11.2432
465.2246-0.4174-0.82592.26651.17852.6815-0.0648-0.6632-0.13630.46340.0296-0.5098-0.05510.94130.0352-0.19080.0877-0.34940.4689-0.2008-0.2429-26.352464.301-13.0463
471.05860.70930.02821.0601-0.77264.6440.1926-1.07590.02060.65660.11160.25180.04230.3065-0.30420.0549-0.05560.05370.2071-0.2223-0.2428-59.829373.39336.6343
483.61290.3298-1.30791.2904-0.08712.19130.00090.09870.0277-0.3656-0.0088-0.645-0.09280.70110.0079-0.2277-0.0761-0.0050.4007-0.22870.0431-5.063972.8359-49.6978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 402 - 40
2X-RAY DIFFRACTION1AA325 - 502325 - 502
3X-RAY DIFFRACTION2AA41 - 13341 - 133
4X-RAY DIFFRACTION3AA134 - 180134 - 180
5X-RAY DIFFRACTION3AA272 - 324272 - 324
6X-RAY DIFFRACTION4AA181 - 271181 - 271
7X-RAY DIFFRACTION5AA570 - 672570 - 672
8X-RAY DIFFRACTION6AA673 - 723673 - 723
9X-RAY DIFFRACTION6AA812 - 859812 - 859
10X-RAY DIFFRACTION7AA724 - 811724 - 811
11X-RAY DIFFRACTION8AA503 - 569503 - 569
12X-RAY DIFFRACTION8AA860 - 1033860 - 1033
13X-RAY DIFFRACTION9BB2 - 402 - 40
14X-RAY DIFFRACTION9BB325 - 502325 - 502
15X-RAY DIFFRACTION10BB41 - 13341 - 133
16X-RAY DIFFRACTION11BB134 - 180134 - 180
17X-RAY DIFFRACTION11BB272 - 324272 - 324
18X-RAY DIFFRACTION12BB181 - 271181 - 271
19X-RAY DIFFRACTION13BB570 - 672570 - 672
20X-RAY DIFFRACTION14BB673 - 723673 - 723
21X-RAY DIFFRACTION14BB812 - 859812 - 859
22X-RAY DIFFRACTION15BB724 - 811724 - 811
23X-RAY DIFFRACTION16BB503 - 569503 - 569
24X-RAY DIFFRACTION16BB860 - 1033860 - 1033
25X-RAY DIFFRACTION17CC2 - 402 - 40
26X-RAY DIFFRACTION17CC325 - 502325 - 502
27X-RAY DIFFRACTION18CC41 - 13341 - 133
28X-RAY DIFFRACTION19CC134 - 180134 - 180
29X-RAY DIFFRACTION19CC272 - 324272 - 324
30X-RAY DIFFRACTION20CC181 - 271181 - 271
31X-RAY DIFFRACTION21CC570 - 672570 - 672
32X-RAY DIFFRACTION22CC673 - 723673 - 723
33X-RAY DIFFRACTION22CC812 - 859812 - 859
34X-RAY DIFFRACTION23CC724 - 811724 - 811
35X-RAY DIFFRACTION24CC503 - 569503 - 569
36X-RAY DIFFRACTION24CC860 - 1033860 - 1033
37X-RAY DIFFRACTION25DD2 - 402 - 40
38X-RAY DIFFRACTION25DD325 - 502325 - 502
39X-RAY DIFFRACTION26DD41 - 13341 - 133
40X-RAY DIFFRACTION27DD134 - 180134 - 180
41X-RAY DIFFRACTION27DD272 - 324272 - 324
42X-RAY DIFFRACTION28DD181 - 271181 - 271
43X-RAY DIFFRACTION29DD570 - 672570 - 672
44X-RAY DIFFRACTION30DD673 - 723673 - 723
45X-RAY DIFFRACTION30DD812 - 859812 - 859
46X-RAY DIFFRACTION31DD724 - 811724 - 811
47X-RAY DIFFRACTION32DD503 - 569503 - 569
48X-RAY DIFFRACTION32DD860 - 1033860 - 1033
49X-RAY DIFFRACTION33EE2 - 402 - 40
50X-RAY DIFFRACTION33EE325 - 502325 - 502
51X-RAY DIFFRACTION34EE41 - 13341 - 133
52X-RAY DIFFRACTION35EE134 - 180134 - 180
53X-RAY DIFFRACTION35EE272 - 324272 - 324
54X-RAY DIFFRACTION36EE181 - 271181 - 271
55X-RAY DIFFRACTION37EE570 - 672570 - 672
56X-RAY DIFFRACTION38EE673 - 723673 - 723
57X-RAY DIFFRACTION38EE812 - 859812 - 859
58X-RAY DIFFRACTION39EE724 - 811724 - 811
59X-RAY DIFFRACTION40EE503 - 569503 - 569
60X-RAY DIFFRACTION40EE860 - 1033860 - 1033
61X-RAY DIFFRACTION41FF2 - 402 - 40
62X-RAY DIFFRACTION41FF325 - 502325 - 502
63X-RAY DIFFRACTION42FF41 - 13341 - 133
64X-RAY DIFFRACTION43FF134 - 180134 - 180
65X-RAY DIFFRACTION43FF272 - 324272 - 324
66X-RAY DIFFRACTION44FF181 - 271181 - 271
67X-RAY DIFFRACTION45FF570 - 672570 - 672
68X-RAY DIFFRACTION46FF673 - 723673 - 723
69X-RAY DIFFRACTION46FF812 - 859812 - 859
70X-RAY DIFFRACTION47FF724 - 811724 - 811
71X-RAY DIFFRACTION48FF503 - 569503 - 569
72X-RAY DIFFRACTION48FF860 - 1033860 - 1033

+
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://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

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