[English] 日本語
Yorodumi
- PDB-5sv1: Structure of the ExbB/ExbD complex from E. coli at pH 4.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5sv1
TitleStructure of the ExbB/ExbD complex from E. coli at pH 4.5
Components
  • Biopolymer transport protein ExbB
  • Biopolymer transport protein ExbD
KeywordsTRANSPORT PROTEIN / ExbB / membrane proteins / pore / channel
Function / homology
Function and homology information


energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / protein import / transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / protein transport ...energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / protein import / transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / protein transport / intracellular iron ion homeostasis / membrane => GO:0016020 / protein stabilization / protein homodimerization activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
TonB-system energizer ExbB type-1 / TonB system transport protein ExbD type-1 / Biopolymer transport protein ExbD/TolR / Biopolymer transport protein ExbD/TolR / MotA/TolQ/ExbB proton channel / MotA/TolQ/ExbB proton channel family
Similarity search - Domain/homology
: / Biopolymer transport protein ExbB / Biopolymer transport protein ExbB / Biopolymer transport protein ExbD / Biopolymer transport protein ExbD
Similarity search - Component
Biological speciesEscherichia coli DH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsCelia, H. / Botos, I. / Lloubes, R. / Buchanan, S.K. / Noinaj, N.
Funding support United States, France, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1K22AI113078-01 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIA DK036139-10 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH GM 038323 United States
French National Research AgencyANR-14-CE09-0023 France
Projets internationaux de cooperation scientifiquePICS05853 France
CitationJournal: Nature / Year: 2016
Title: Structural insight into the role of the Ton complex in energy transduction.
Authors: Celia, H. / Noinaj, N. / Zakharov, S.D. / Bordignon, E. / Botos, I. / Santamaria, M. / Barnard, T.J. / Cramer, W.A. / Lloubes, R. / Buchanan, S.K.
History
DepositionAug 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_detector ...citation / diffrn_detector / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 4, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Biopolymer transport protein ExbB
B: Biopolymer transport protein ExbB
C: Biopolymer transport protein ExbB
D: Biopolymer transport protein ExbB
E: Biopolymer transport protein ExbB
F: Biopolymer transport protein ExbB
G: Biopolymer transport protein ExbB
H: Biopolymer transport protein ExbB
I: Biopolymer transport protein ExbB
J: Biopolymer transport protein ExbB
Y: Biopolymer transport protein ExbD
Z: Biopolymer transport protein ExbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,24022
Polymers276,23512
Non-polymers2,00610
Water00
1
A: Biopolymer transport protein ExbB
B: Biopolymer transport protein ExbB
C: Biopolymer transport protein ExbB
D: Biopolymer transport protein ExbB
E: Biopolymer transport protein ExbB
Y: Biopolymer transport protein ExbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,12011
Polymers138,1176
Non-polymers1,0035
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18420 Å2
ΔGint-243 kcal/mol
Surface area51130 Å2
MethodPISA
2
F: Biopolymer transport protein ExbB
G: Biopolymer transport protein ExbB
H: Biopolymer transport protein ExbB
I: Biopolymer transport protein ExbB
J: Biopolymer transport protein ExbB
Z: Biopolymer transport protein ExbD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,12011
Polymers138,1176
Non-polymers1,0035
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18280 Å2
ΔGint-240 kcal/mol
Surface area51540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.942, 196.748, 210.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Biopolymer transport protein ExbB


Mass: 26339.367 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH1 (bacteria) / Gene: exbB / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABU8, UniProt: P0ABU7*PLUS
#2: Protein Biopolymer transport protein ExbD


Mass: 6420.452 Da / Num. of mol.: 2 / Fragment: UNP residues 1-49
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH1 (bacteria) / Gene: exbD / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABV4, UniProt: P0ABV2*PLUS
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Hg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.94 Å3/Da / Density % sol: 68.74 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 100 mM Na-acetate, pH 4.5, 100 mM MgCl2, and 25% PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.007 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 3.5→49 Å / Num. obs: 55966 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rsym value: 0.24 / Net I/σ(I): 8.9
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
DENZOHKL2000data reduction
SCALEPACKHKL2000data scaling
PHASERPHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5SV0
Resolution: 3.5→49 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.1
RfactorNum. reflection% reflection
Rfree0.2996 1995 3.56 %
Rwork0.2546 --
obs0.2561 55966 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16936 0 10 0 16946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817187
X-RAY DIFFRACTIONf_angle_d0.96523272
X-RAY DIFFRACTIONf_dihedral_angle_d18.07710202
X-RAY DIFFRACTIONf_chiral_restr0.0522771
X-RAY DIFFRACTIONf_plane_restr0.0062996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.55720.3843980.35572976X-RAY DIFFRACTION76
3.5572-3.65330.39521650.353846X-RAY DIFFRACTION100
3.6533-3.76080.41441250.35463894X-RAY DIFFRACTION100
3.7608-3.88220.33861460.30533889X-RAY DIFFRACTION100
3.8822-4.02080.30421520.29343860X-RAY DIFFRACTION100
4.0208-4.18170.30021380.27963899X-RAY DIFFRACTION100
4.1817-4.3720.29531480.24773910X-RAY DIFFRACTION100
4.372-4.60230.26091410.2333876X-RAY DIFFRACTION100
4.6023-4.89040.29311380.22183932X-RAY DIFFRACTION100
4.8904-5.26760.24661490.22153914X-RAY DIFFRACTION99
5.2676-5.7970.31811490.25533926X-RAY DIFFRACTION100
5.797-6.63410.31511500.26953959X-RAY DIFFRACTION100
6.6341-8.35160.25731440.23323994X-RAY DIFFRACTION99
8.3516-49.29580.26941520.19924096X-RAY DIFFRACTION98
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)
10.17880.86061.75464.71063.89063.8488-0.26820.07870.1447-1.11930.0289-0.2644-0.92630.40760.13390.8331-0.15180.34260.9544-0.15371.15670.501392.381225.3658
21.6325-0.0774-0.53543.08863.38381.284-0.58-0.03330.58580.50730.46240.59420.6930.05990.11451.04150.1099-0.05610.7642-0.04170.945964.84296.303841.6324
30.34080.2217-0.21950.2431-0.33331.1010.16620.38150.22360.87930.89341.3607-0.5447-0.7056-0.82811.2679-0.91680.38251.61260.33122.50361.4822132.566568.2334
40.61860.94430.97332.44512.12172.36740.17320.0502-0.0342-0.17060.6775-1.1598-0.46130.254-0.55510.9581-0.05840.24190.7903-0.15120.73261.46992.334627.4236
51.10180.45671.69251.66270.62622.67260.4138-1.0876-0.42561.3646-0.38760.32720.41160.3445-0.33051.1995-0.05670.13270.8556-0.32131.289864.1165111.424374.4169
6-0.4419-0.0492-1.40175.81115.00293.01770.10970.02820.21020.13320.381-0.6754-0.34860.2103-0.49280.74260.0340.24781.1317-0.25290.911870.403286.491353.6165
71.980.1367-0.67783.9981.41091.88390.4562-0.46260.13710.4748-0.2127-0.47390.4502-0.2346-0.32030.6904-0.0015-0.07650.80480.06610.461165.382962.59539.5308
82.40520.7462-0.4472.142-0.35913.3249-0.6046-0.90020.09271.04350.03661.22750.57730.36980.42280.559-0.03010.23490.9521-0.34251.07552.1398111.127865.4932
90.69620.4074-1.60331.15242.56880.9998-0.046-0.04660.43840.1006-0.15270.56010.84770.9856-0.50230.78180.0043-0.17520.7536-0.47231.138665.379181.985942.6626
101.1183-0.6568-1.00882.26950.54420.9843-0.0439-0.6096-0.7591-0.1531-0.50411.49050.2852-0.72020.02341.2242-0.36720.01631.1434-0.19541.277636.0042111.243872.9652
11-0.1992-1.4492-1.16295.36633.0220.3668-0.3331-0.14230.14860.98680.377-0.09710.32110.07720.25331.0862-0.0034-0.0751.2187-0.22141.115143.159182.270961.2429
123.82181.99532.05851.4558-0.05795.98380.49230.034-1.2184-0.8394-0.7043-0.01542.087-2.0611-0.03971.2016-0.31230.02750.88170.03120.648944.98855.288153.2098
133.25910.51373.01732.11011.04563.51520.1254-0.6010.51980.2145-0.33610.0881-0.3287-0.78790.11690.5569-0.08970.18890.6143-0.06170.886440.300862.784240.7473
141.5441-0.68660.32223.66730.53663.0068-0.7286-0.6641-0.0175-0.04221.05231.5074-0.81180.3050.04970.85670.2323-0.15621.0908-0.62441.578438.03113.372557.7627
150.8883-0.38140.54663.61771.46230.7864-0.0635-0.2721-0.018-0.37820.322-0.7845-0.2373-0.0510.02930.8566-0.1410.14950.8545-0.14210.550547.612381.843251.1216
162.1071-0.4478-1.33062.64682.09020.7021-0.40370.05140.83250.50440.4710.50470.1987-0.08290.01260.76230.0428-0.01120.8339-0.12450.775624.458294.748940.1088
173.1531-1.1291-0.93642.55191.02795.03620.05130.15960.4122-0.18070.0893-0.2057-0.1349-0.3455-0.18310.5266-0.01440.05060.4677-0.04780.734229.408170.523324.8393
188.52450.8791.35884.52611.80552.4621-0.8260.05820.6819-0.41981.9894-1.1383-0.68650.6197-0.33470.8374-0.04150.17960.8211-0.10811.18840.0091121.828545.1305
19-0.1610.67660.75669.60153.96641.5636-0.4036-0.11440.41280.22050.9876-0.74270.05420.4519-0.54120.6813-0.12760.14880.65-0.24721.138733.207485.159339.0793
20-2.50241.61290.95283.55921.02261.6487-0.375-0.17581.6002-0.1056-0.2230.9371-0.0183-0.08410.45550.94620.1301-0.1320.9883-0.3841.534244.869591.994915.232
211.40830.49181.60080.3141-0.1924.3837-0.54270.19121.01350.74380.5746-0.16530.57491.8126-0.21360.7957-0.1421-0.18470.9023-0.28681.479555.6974122.462544.1565
222.8066-0.62450.69281.24591.5099-0.13080.1387-0.18030.5622-0.2627-0.99680.5988-0.0819-0.69540.62571.0744-0.02280.18840.55070.17730.788942.476893.285324.6745
230.48110.11681.89450.6554-0.62128.6681-0.48760.05160.17310.22-0.2356-0.67-0.23561.73470.78051.32980.03490.1951.0903-0.09441.9297125.339680.087253.2422
24-0.2412-0.4741-0.34672.16781.56891.5349-0.4402-0.1105-0.32711.11130.4838-0.71510.66190.6533-0.24521.03720.1741-0.29431.0119-0.32641.3654122.3399119.151883.9609
25-0.62950.5435-0.54042.61622.7311.5487-0.54470.1111-0.1349-0.49330.48790.4687-0.43150.7537-0.04671.05080.2801-0.21960.9766-0.3470.663117.2775111.079863.9381
261.4615-1.5474-0.87055.10873.31832.3342-0.01660.0393-0.32410.61090.4738-1.34610.30810.4225-0.1690.95940.0645-0.08770.6406-0.21971.2312113.8249111.799375.0028
271.0218-0.1545-0.94680.16420.29680.98460.91631.4329-0.2496-1.7291-1.0491-0.6719-1.70450.1168-0.54521.04460.0941-0.05311.3777-0.27561.3858116.393796.048831.1102
280.2584-0.92040.61674.67313.22731.8569-0.05690.3963-0.1523-0.44760.2642-0.5803-0.35640.5604-0.40120.7831-0.0520.25610.9687-0.27911.4213122.7999120.777451.7534
295.4969-2.8433-1.00473.26431.15691.8875-0.15180.39280.2916-0.35150.0130.0315-0.09440.29560.16160.6323-0.09110.16910.6103-0.01421.1501117.8203144.450166.1492
302.6384-1.20841.55821.5079-1.26061.65020.14880.3365-0.6667-0.1280.41710.14490.08610.3998-0.39230.62960.04930.03610.9007-0.38551.0601104.663396.563539.8326
310.14031.36250.9152.15141.57611.8834-0.14250.3185-0.14120.24930.53170.1352-0.00220.7775-0.4490.58130.01880.04780.7069-0.17311.2377117.8197125.318763.067
320.6340.96290.75281.56761.15570.8292-0.43290.2847-0.39680.70570.09351.004-0.9547-1.2928-0.02181.21780.24340.261.8405-0.06491.318188.202296.133232.3627
331.07810.1199-0.08924.76093.10490.2837-0.22610.2609-0.1902-1.37220.642-0.6252-0.59770.2185-0.18011.1103-0.06420.08171.011-0.1970.761795.9329125.473644.1362
342.711-0.8303-1.88083.69681.38714.96390.67610.2777-0.1849-1.0022-0.2220.3591-1.6281-0.45310.10830.62370.08050.10620.7190.03540.646694.6482151.769960.0131
355.0401-1.03490.04682.24530.80635.85020.81210.8387-2.78040.7089-0.0095-0.29731.64510.42270.91120.43360.18040.52920.99460.2809-0.827393.273138.276564.0127
361.46420.5109-0.27613.0657-0.28162.2184-0.62990.9629-0.83161.40570.7850.90430.99460.1856-0.22331.00070.0089-0.18550.9719-0.38581.052290.460593.844247.2141
370.49790.54280.46135.26563.29512.39130.40860.3078-0.14470.2432-0.2842-1.21820.167-0.1361-0.19850.66790.089-0.03530.7394-0.07320.7769100.025124.953853.9653
382.45931.65120.50121.29011.79962.1531-0.3837-0.41990.255-0.06230.7352-1.3824-0.02530.2338-0.10150.67480.0183-0.00890.6491-0.11051.23276.9638112.623764.9469
393.6603-1.08460.55152.0121.72282.4265-0.4766-1.1925-0.61250.82340.8075-0.37520.3161-0.2809-0.1160.7550.1055-0.00311.3208-0.0511-0.189181.7966136.683480.3141
403.47490.54491.4812.110.15223.5169-0.58890.364-0.61591.12761.4944-0.83111.02160.8586-0.41840.76960.00840.05690.6713-0.26971.23692.465585.159759.8833
410.3661-0.4933-0.33083.86541.1679-0.17810.5063-0.2353-3.6003-0.4623-0.24431.5601-0.40330.41870.19320.88830.12590.11570.6891-0.3192-1.240285.6184122.951566.3042
42-0.3102-1.642-0.48374.19452.26760.741-0.00560.4251-0.26891.1063-0.2785-0.66190.7757-0.57650.39321.01580.1271-0.15870.7407-0.15041.350795.1183100.87183.2661
433.96931.0322-0.42425.76720.29013.40020.3246-0.5786-0.24950.7225-0.0752-1.04970.01190.2599-0.19080.79960.0975-0.21980.62830.11690.746597.923127.830495.35
441.2818-0.2576-0.82994.58361.9644.6816-1.1987-0.2889-1.0092-1.64861.51680.5278-1.05581.1462-0.14180.769-0.01470.22410.9772-0.56991.8576108.17385.39261.1942
450.912-1.20660.10872.36011.57371.5062-0.3461-0.0274-0.3472-0.60961.1121-0.4814-0.50890.8742-0.63580.9659-0.02930.17910.6469-0.2030.713194.8272114.164580.3398
46-0.0408-0.07660.1294-0.04020.1742-0.1550.7131-1.11240.76671.2062-1.04270.93770.11940.04530.13161.3429-0.19510.32741.5954-0.17951.370450.4283118.543254.1517
471.5262-0.93071.4870.7478-0.70711.45490.89610.9192-1.1688-0.4252-0.32030.87211.0325-1.6889-0.32520.8838-0.33360.0861.70930.11961.4161102.680788.990150.0004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 161 )
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 168 )
4X-RAY DIFFRACTION4chain 'A' and (resid 169 through 234 )
5X-RAY DIFFRACTION5chain 'B' and (resid 10 through 20 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 64 )
7X-RAY DIFFRACTION7chain 'B' and (resid 65 through 129 )
8X-RAY DIFFRACTION8chain 'B' and (resid 130 through 170 )
9X-RAY DIFFRACTION9chain 'B' and (resid 171 through 234 )
10X-RAY DIFFRACTION10chain 'C' and (resid 10 through 21 )
11X-RAY DIFFRACTION11chain 'C' and (resid 22 through 64 )
12X-RAY DIFFRACTION12chain 'C' and (resid 65 through 82 )
13X-RAY DIFFRACTION13chain 'C' and (resid 83 through 129 )
14X-RAY DIFFRACTION14chain 'C' and (resid 130 through 166 )
15X-RAY DIFFRACTION15chain 'C' and (resid 167 through 233 )
16X-RAY DIFFRACTION16chain 'D' and (resid 19 through 64 )
17X-RAY DIFFRACTION17chain 'D' and (resid 65 through 129 )
18X-RAY DIFFRACTION18chain 'D' and (resid 130 through 170 )
19X-RAY DIFFRACTION19chain 'D' and (resid 171 through 233 )
20X-RAY DIFFRACTION20chain 'E' and (resid 12 through 129 )
21X-RAY DIFFRACTION21chain 'E' and (resid 130 through 169 )
22X-RAY DIFFRACTION22chain 'E' and (resid 170 through 234 )
23X-RAY DIFFRACTION23chain 'F' and (resid 9 through 20 )
24X-RAY DIFFRACTION24chain 'F' and (resid 21 through 105 )
25X-RAY DIFFRACTION25chain 'F' and (resid 106 through 161 )
26X-RAY DIFFRACTION26chain 'F' and (resid 162 through 234 )
27X-RAY DIFFRACTION27chain 'G' and (resid 10 through 20 )
28X-RAY DIFFRACTION28chain 'G' and (resid 21 through 64 )
29X-RAY DIFFRACTION29chain 'G' and (resid 65 through 129 )
30X-RAY DIFFRACTION30chain 'G' and (resid 130 through 170 )
31X-RAY DIFFRACTION31chain 'G' and (resid 171 through 234 )
32X-RAY DIFFRACTION32chain 'H' and (resid 11 through 21 )
33X-RAY DIFFRACTION33chain 'H' and (resid 22 through 64 )
34X-RAY DIFFRACTION34chain 'H' and (resid 65 through 105 )
35X-RAY DIFFRACTION35chain 'H' and (resid 106 through 129 )
36X-RAY DIFFRACTION36chain 'H' and (resid 130 through 166 )
37X-RAY DIFFRACTION37chain 'H' and (resid 167 through 232 )
38X-RAY DIFFRACTION38chain 'I' and (resid 19 through 64 )
39X-RAY DIFFRACTION39chain 'I' and (resid 65 through 129 )
40X-RAY DIFFRACTION40chain 'I' and (resid 130 through 170 )
41X-RAY DIFFRACTION41chain 'I' and (resid 171 through 234 )
42X-RAY DIFFRACTION42chain 'J' and (resid 16 through 64 )
43X-RAY DIFFRACTION43chain 'J' and (resid 65 through 129 )
44X-RAY DIFFRACTION44chain 'J' and (resid 130 through 169 )
45X-RAY DIFFRACTION45chain 'J' and (resid 170 through 234 )
46X-RAY DIFFRACTION46chain 'Y' and (resid 3 through 25 )
47X-RAY DIFFRACTION47chain 'Z' and (resid 3 through 24 )

+
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