[English] 日本語
Yorodumi
- PDB-7th2: Single-domain VHH intrabodies neutralize ricin toxin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7th2
TitleSingle-domain VHH intrabodies neutralize ricin toxin
Components
  • Ricin A chain
  • VHH antibody
KeywordsIMMUNE SYSTEM/TOXIN / Antibody-antigen complex / IMMUNE SYSTEM / IMMUNE SYSTEM-TOXIN complex
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function
Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil ...Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.838 Å
AuthorsRudolph, M.J. / Mantis, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400021C United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Single-domain antibodies neutralize ricin toxin intracellularly by blocking access to ribosomal P-stalk proteins.
Authors: Czajka, T.F. / Vance, D.J. / Davis, S. / Rudolph, M.J. / Mantis, N.J.
History
DepositionJan 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ricin A chain
B: Ricin A chain
C: VHH antibody
D: VHH antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,35932
Polymers88,8124
Non-polymers1,54728
Water9,764542
1
A: Ricin A chain
C: VHH antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,08715
Polymers44,4062
Non-polymers68113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-115 kcal/mol
Surface area17750 Å2
MethodPISA
2
B: Ricin A chain
D: VHH antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,27217
Polymers44,4062
Non-polymers86615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-104 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.644, 63.812, 99.298
Angle α, β, γ (deg.)90.000, 107.120, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -1 through 84 or resid 86...
21(chain B and (resid -1 through 84 or resid 86...
12(chain C and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))
22(chain D and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALATYRTYR(chain A and (resid -1 through 84 or resid 86...AA-1 - 841 - 86
121ALAALATYRTYR(chain A and (resid -1 through 84 or resid 86...AA86 - 12388 - 125
131ARGARGGLYGLY(chain A and (resid -1 through 84 or resid 86...AA125 - 158127 - 160
141GLNGLNARGARG(chain A and (resid -1 through 84 or resid 86...AA160 - 258162 - 260
211ALAALATYRTYR(chain B and (resid -1 through 84 or resid 86...BB-1 - 841 - 86
221ALAALATYRTYR(chain B and (resid -1 through 84 or resid 86...BB86 - 12388 - 125
231ARGARGGLYGLY(chain B and (resid -1 through 84 or resid 86...BB125 - 158127 - 160
241GLNGLNARGARG(chain B and (resid -1 through 84 or resid 86...BB160 - 258162 - 260
112GLNGLNSERSER(chain C and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))CC3 - 483 - 48
122ILEILEVALVAL(chain C and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))CC50 - 10450 - 104
132THRTHRSERSER(chain C and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))CC106 - 124106 - 124
212GLNGLNSERSER(chain D and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))DD3 - 483 - 48
222ILEILEVALVAL(chain D and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))DD50 - 10450 - 104
232THRTHRSERSER(chain D and (resid 3 through 48 or resid 50 through 104 or resid 106 through 124))DD106 - 124106 - 124

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Ricin A chain / rRNA N-glycosidase


Mass: 30139.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: P02879, rRNA N-glycosylase
#2: Protein VHH antibody


Mass: 14266.763 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): 'BL21-Gold(DE3)pLysS AG'

-
Non-polymers , 5 types, 570 molecules

#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 100 mM MES pH 6.5, 200 mM sodium thiocyanate, 8% dioxane, 1740 mM ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 61630 / % possible obs: 98 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.051 / Rrim(I) all: 0.126 / Χ2: 1.369 / Net I/σ(I): 8.5 / Num. measured all: 372877
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.866.10.90730230.8410.3920.9910.43696.8
1.86-1.96.10.74330040.870.3230.8120.49796.8
1.9-1.9360.6130660.9130.2660.6670.57498.5
1.93-1.976.10.47730660.930.2090.5220.60998.1
1.97-2.016.20.4130800.9570.1790.4490.65898.3
2.01-2.0660.34931020.9580.1540.3830.74899
2.06-2.1160.330620.9650.1340.3290.75298.6
2.11-2.175.90.24130980.9760.1080.2650.84298.5
2.17-2.235.60.21830880.9630.10.2410.9598.2
2.23-2.315.30.17728890.980.0840.1971.08392.3
2.31-2.396.30.17830700.9850.0780.1941.01198.6
2.39-2.486.50.15931290.9880.0680.1731.10199.1
2.48-2.66.40.14331150.9880.0620.1561.31299.1
2.6-2.736.20.12831380.9880.0570.1411.53999.1
2.73-2.96.10.11130910.990.0490.1221.83198.8
2.9-3.135.90.09231050.9930.0420.1012.23898.8
3.13-3.445.40.07529960.9930.0360.0842.71594.8
3.44-3.946.40.06331790.9960.0270.0692.92299.7
3.94-4.976.20.05331500.9960.0230.0582.84499.2
4.97-506.10.04631790.9980.020.0512.52497.3

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RTC, 4LGR

1rtc

4lgr


Resolution: 1.838→47.449 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 17.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1874 3189 5.18 %
Rwork0.1487 58396 -
obs0.1507 61585 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.55 Å2 / Biso mean: 31.9007 Å2 / Biso min: 8.23 Å2
Refinement stepCycle: final / Resolution: 1.838→47.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6034 0 106 542 6682
Biso mean--54.85 35.11 -
Num. residues----773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086265
X-RAY DIFFRACTIONf_angle_d0.9118529
X-RAY DIFFRACTIONf_chiral_restr0.054930
X-RAY DIFFRACTIONf_plane_restr0.0071117
X-RAY DIFFRACTIONf_dihedral_angle_d11.043726
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3116X-RAY DIFFRACTION7.659TORSIONAL
12B3116X-RAY DIFFRACTION7.659TORSIONAL
21C1354X-RAY DIFFRACTION7.659TORSIONAL
22D1354X-RAY DIFFRACTION7.659TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.838-1.86520.2441270.1929211183
1.8652-1.89440.22621470.1752248796
1.8944-1.92540.22341360.1711253998
1.9254-1.95860.21431640.1543254198
1.9586-1.99420.1961220.1573254299
1.9942-2.03260.24161480.154255598
2.0326-2.07410.19211420.1531258199
2.0741-2.11920.17721360.1462254299
2.1192-2.16850.16951360.143256198
2.1685-2.22270.19331310.1455257299
2.2227-2.28280.1851510.1401245995
2.2828-2.350.20171340.1456243495
2.35-2.42580.18131340.1454260599
2.4258-2.51250.2011280.1514259999
2.5125-2.61310.17691350.1454257899
2.6131-2.7320.16021220.1505258399
2.732-2.87610.1841280.1496261599
2.8761-3.05620.20491330.1534259099
3.0562-3.29210.20451540.1532248596
3.2921-3.62330.17161530.1417253197
3.6233-4.14740.181550.13412619100
4.1474-5.22420.14971480.1269261999
5.2242-47.4490.2131250.1777264897
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)
11.1228-0.6222-0.70381.27480.45530.50320.0537-0.1370.13510.03250.0033-0.1615-0.0862-0.0635-0.0340.1328-0.0071-0.00040.1290.00770.148-41.6903-4.004982.6405
24.0951.75932.67552.52612.39834.7541-0.0918-0.09630.20790.0027-0.04160.0918-0.1794-0.21840.14430.08590.0040.0190.07540.00610.1055-48.7732-5.116287.9982
33.8092-0.0946-1.19133.96830.34792.22530.1319-0.1450.18040.3689-0.01740.2644-0.1506-0.2127-0.04480.13280.01120.03280.14210.01460.1456-55.6487-7.595595.3284
41.9153-0.4353-0.30280.8269-0.30371.3692-0.07150.0811-0.3073-0.0547-0.02190.15370.2059-0.23180.10450.1299-0.03880.01160.1281-0.0280.1737-50.9172-21.099482.696
52.2152-0.00140.31593.150.40382.5735-0.0966-0.258-0.18280.24930.0631-0.19530.24110.27590.02630.16280.0402-0.00340.17250.0510.1579-30.1585-22.200891.5513
61.39170.65760.54692.71271.29972.08170.09970.2858-0.3308-0.1396-0.0747-0.02490.0738-0.3416-0.0840.13040.0032-0.02550.2013-0.0320.1401-30.8791-5.577259.5686
74.95372.47861.98593.3431.9293.171-0.01540.4462-0.4477-0.32110.0879-0.60970.13960.3566-0.06110.31640.01550.07060.4615-0.00710.2876-19.6025-0.282145.9103
83.3335-1.20490.0221.79390.0632.42880.12710.75680.0402-0.3616-0.11210.07610.1229-0.16670.02740.18180.0043-0.02660.36090.02650.1346-39.84461.777149.2498
93.1193-0.0655-0.12220.7566-0.17831.3195-0.06660.12770.61260.03840.05820.0282-0.1882-0.22630.03650.16180.0281-0.00830.14730.03860.2149-36.286511.648662.2309
101.77590.0281.08592.25980.08430.627-0.04040.71980.6645-0.365-0.0325-0.3901-0.2770.3426-0.05450.2421-0.0540.03410.33730.15280.4084-15.366616.045253.8002
112.68111.7091-0.36355.3129-1.64747.1644-0.04660.7704-0.2053-0.32950.00860.610.4763-0.42130.15120.2249-0.0463-0.03870.2166-0.11090.2443-26.9224-22.609860.733
126.01360.32643.05891.95020.67293.2897-0.05790.19940.3509-0.1569-0.0523-0.056-0.11110.28760.08890.1321-0.01590.02330.1340.01620.1261-11.5574-17.704464.1149
134.5699-2.14281.36262.7748-1.43724.93470.0022-0.1395-0.3004-0.04470.06360.3307-0.0984-0.3396-0.05180.0986-0.02830.00930.0692-0.03660.1351-26.0081-21.060668.4388
143.712-3.365-2.96636.03274.25553.2287-0.1692-0.3274-0.46020.03310.06490.03090.63130.40920.01240.26870.06890.01980.13330.01490.2497-16.7038-28.704573.2186
152.8401-4.5633-0.14698.00650.13735.8577-0.0182-0.33550.04830.13960.07180.1427-0.03470.2702-0.07390.1311-0.01780.02260.1066-0.00210.1413-21.4373-17.514578.8197
167.63-3.89936.59284.0383-2.83167.848-0.1111-0.01310.05590.01420.1459-0.0305-0.2330.00860.01970.11-0.0250.0220.1052-0.01750.1125-19.0144-13.910969.8358
175.94051.4683-1.21460.83190.11551.0883-0.0468-0.0962-0.18090.1440.0514-0.03310.01850.10070.02750.14140.02880.00780.07930.00420.1479-18.0443-24.714172.8829
185.67730.2087-0.97735.8712-0.11268.0879-0.09620.0849-0.62380.07590.06680.53160.6126-0.50840.16350.1517-0.03760.01860.1022-0.06680.2617-27.0858-28.983468.1712
191.99-0.3685-2.25344.5754-0.92572.9645-0.29480.6713-0.68650.1440.1761-0.6754-0.03620.94180.12090.1783-0.01760.01340.4138-0.06040.2745-0.5305-23.163764.7216
205.1629-0.2480.79714.0811-0.0484.3497-0.0982-0.0098-0.26990.11830.02250.20260.1582-0.12210.09590.1314-0.0049-0.010.10540.02220.11230.92893.3279.4443
210.851-0.7931-0.87123.8256-2.05383.56560.7068-1.777-0.87270.774-0.67610.31550.5797-0.5155-0.21320.2955-0.1576-0.04310.51470.0960.345-18.43692.311777.1874
225.77794.07921.53175.90730.38362.0766-0.121-0.2320.82090.2697-0.1260.2193-0.0896-0.07440.11390.11860.0093-0.01910.0792-0.02420.1705-4.429611.829375.1715
231.73061.81053.22551.96833.37426.0188-0.3045-0.16690.8278-0.0611-0.3214-0.11-0.90870.05910.35960.3212-0.0588-0.12730.1496-0.03240.4769-2.019516.129973.9507
245.57640.73222.35631.61070.8823.2581-0.07840.46210.21750.0116-0.0260.0273-0.08340.26530.07130.14370.0029-0.01130.15260.03110.1732-4.19067.565764.6763
254.4166-1.2697-1.33131.9463-1.27656.40320.09490.0008-0.4521-0.0440.06530.19990.6277-0.3070.00390.2244-0.0237-0.02880.17050.01760.2355-5.7006-0.102172.9333
267.6703-1.63360.44491.52751.07822.3566-0.1099-0.12840.3604-0.03230.0227-0.1106-0.09320.180.08510.1507-0.0233-0.00640.1060.01780.15883.100110.325375.5217
276.904-0.3996-0.72372.9856-1.81874.9705-0.18390.04240.6686-0.1887-0.1846-0.1064-0.27160.1050.28060.1870.0222-0.06710.1184-0.00980.2598-13.228815.288668.0047
282.83040.2888-0.96744.04052.25112.3304-0.2135-0.70530.31310.1159-0.09330.319-0.7524-0.5813-0.14190.19990.071-0.02670.2768-0.12220.2518-12.175514.585478.6472
294.5473-0.6019-1.36817.591-0.5486.2391-0.1948-0.57750.4621-0.07510.1361-0.47270.05570.89540.03720.11820.0037-0.02890.2124-0.01950.15789.43148.949381.2352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 44 )A-1 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 75 )A45 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 122 )A76 - 122
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 201 )A123 - 201
5X-RAY DIFFRACTION5chain 'A' and (resid 202 through 258 )A202 - 258
6X-RAY DIFFRACTION6chain 'B' and (resid -1 through 33 )B-1 - 33
7X-RAY DIFFRACTION7chain 'B' and (resid 34 through 56 )B34 - 56
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 122 )B57 - 122
9X-RAY DIFFRACTION9chain 'B' and (resid 123 through 201 )B123 - 201
10X-RAY DIFFRACTION10chain 'B' and (resid 202 through 261 )B202 - 261
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 7 )C1 - 7
12X-RAY DIFFRACTION12chain 'C' and (resid 8 through 25 )C8 - 25
13X-RAY DIFFRACTION13chain 'C' and (resid 26 through 38 )C26 - 38
14X-RAY DIFFRACTION14chain 'C' and (resid 39 through 50 )C39 - 50
15X-RAY DIFFRACTION15chain 'C' and (resid 51 through 63 )C51 - 63
16X-RAY DIFFRACTION16chain 'C' and (resid 64 through 82 )C64 - 82
17X-RAY DIFFRACTION17chain 'C' and (resid 83 through 107 )C83 - 107
18X-RAY DIFFRACTION18chain 'C' and (resid 108 through 117 )C108 - 117
19X-RAY DIFFRACTION19chain 'C' and (resid 118 through 128 )C118 - 128
20X-RAY DIFFRACTION20chain 'D' and (resid 3 through 24 )D3 - 24
21X-RAY DIFFRACTION21chain 'D' and (resid 25 through 31 )D25 - 31
22X-RAY DIFFRACTION22chain 'D' and (resid 32 through 38 )D32 - 38
23X-RAY DIFFRACTION23chain 'D' and (resid 39 through 50 )D39 - 50
24X-RAY DIFFRACTION24chain 'D' and (resid 51 through 66 )D51 - 66
25X-RAY DIFFRACTION25chain 'D' and (resid 67 through 82 )D67 - 82
26X-RAY DIFFRACTION26chain 'D' and (resid 83 through 98 )D83 - 98
27X-RAY DIFFRACTION27chain 'D' and (resid 99 through 107 )D99 - 107
28X-RAY DIFFRACTION28chain 'D' and (resid 108 through 117 )D108 - 117
29X-RAY DIFFRACTION29chain 'D' and (resid 118 through 124 )D118 - 124

+
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