[English] 日本語
Yorodumi
- PDB-8dn7: The crystal structure of the Pisum sativum Toc75 POTRA domains in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dn7
TitleThe crystal structure of the Pisum sativum Toc75 POTRA domains in complex with fab ax9
Components
  • Protein TOC75, chloroplastic
  • fabax9 Heavy Chain
  • fabax9 Light Chain
KeywordsMembrane Protein/Immune System / Membrane Protein / Chloroplast / Membrane Protein-Immune System complex
Function / homologyChloroplast envelope protein translocase, IAP75 / chloroplast outer membrane / protein-transporting ATPase activity / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / intracellular protein transport / Protein TOC75, chloroplastic
Function and homology information
Biological speciesPisum sativum (garden pea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSrinivasan, K. / Noinaj, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127896-01 United States
CitationJournal: Structure / Year: 2023
Title: Characterization of synthetic antigen binding fragments targeting Toc75 for the isolation of TOC in A. thaliana and P. sativum.
Authors: Srinivasan, K. / Erramilli, S.K. / Chakravarthy, S. / Gonzalez, A. / Kossiakoff, A. / Noinaj, N.
History
DepositionJul 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Protein TOC75, chloroplastic
C: Protein TOC75, chloroplastic
D: fabax9 Heavy Chain
A: fabax9 Heavy Chain
B: fabax9 Light Chain
H: fabax9 Light Chain


Theoretical massNumber of molelcules
Total (without water)171,1806
Polymers171,1806
Non-polymers00
Water7,602422
1
E: Protein TOC75, chloroplastic
D: fabax9 Heavy Chain
H: fabax9 Light Chain


Theoretical massNumber of molelcules
Total (without water)85,5903
Polymers85,5903
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-44 kcal/mol
Surface area24820 Å2
MethodPISA
2
C: Protein TOC75, chloroplastic
A: fabax9 Heavy Chain
B: fabax9 Light Chain


Theoretical massNumber of molelcules
Total (without water)85,5903
Polymers85,5903
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-44 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.212, 43.430, 169.606
Angle α, β, γ (deg.)94.200, 94.210, 104.440
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 194 or resid 196 through 231))
21(chain D and (resid 5 through 132 or (resid 133...
12(chain B and (resid 3 through 10 or resid 12 or resid 14 through 158 or resid 160 through 216))
22(chain H and (resid 3 through 10 or resid 12...
13(chain C and (resid 114 or (resid 115 and (name...
23(chain E and resid 114 through 228)

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
111VALVALLEULEU(chain A and (resid 5 through 194 or resid 196 through 231))AD5 - 1945 - 194
121SERSERSERSER(chain A and (resid 5 through 194 or resid 196 through 231))AD196 - 231196 - 231
211VALVALTHRTHR(chain D and (resid 5 through 132 or (resid 133...DC5 - 1325 - 132
221LYSLYSLYSLYS(chain D and (resid 5 through 132 or (resid 133...DC133133
231VALVALCYSCYS(chain D and (resid 5 through 132 or (resid 133...DC5 - 2325 - 232
241VALVALCYSCYS(chain D and (resid 5 through 132 or (resid 133...DC5 - 2325 - 232
251VALVALCYSCYS(chain D and (resid 5 through 132 or (resid 133...DC5 - 2325 - 232
261VALVALCYSCYS(chain D and (resid 5 through 132 or (resid 133...DC5 - 2325 - 232
112ILEILESERSER(chain B and (resid 3 through 10 or resid 12 or resid 14 through 158 or resid 160 through 216))BE3 - 103 - 10
122LEULEULEULEU(chain B and (resid 3 through 10 or resid 12 or resid 14 through 158 or resid 160 through 216))BE1212
132ALAALAGLNGLN(chain B and (resid 3 through 10 or resid 12 or resid 14 through 158 or resid 160 through 216))BE14 - 15814 - 158
142GLYGLYGLUGLU(chain B and (resid 3 through 10 or resid 12 or resid 14 through 158 or resid 160 through 216))BE160 - 216160 - 216
212ILEILESERSER(chain H and (resid 3 through 10 or resid 12...HF3 - 103 - 10
222LEULEULEULEU(chain H and (resid 3 through 10 or resid 12...HF1212
232ALAALAALAALA(chain H and (resid 3 through 10 or resid 12...HF14 - 2614 - 26
242SERSERGLNGLN(chain H and (resid 3 through 10 or resid 12...HF27 - 2827 - 28
252ILEILECYSCYS(chain H and (resid 3 through 10 or resid 12...HF3 - 2173 - 217
262ILEILECYSCYS(chain H and (resid 3 through 10 or resid 12...HF3 - 2173 - 217
272ILEILECYSCYS(chain H and (resid 3 through 10 or resid 12...HF3 - 2173 - 217
113ALAALAALAALA(chain C and (resid 114 or (resid 115 and (name...CB114115
123ASPASPASPASP(chain C and (resid 114 or (resid 115 and (name...CB115116
133ALAALALYSLYS(chain C and (resid 114 or (resid 115 and (name...CB114 - 231115 - 232
143ALAALALYSLYS(chain C and (resid 114 or (resid 115 and (name...CB114 - 231115 - 232
153ALAALALYSLYS(chain C and (resid 114 or (resid 115 and (name...CB114 - 231115 - 232
163ALAALALYSLYS(chain C and (resid 114 or (resid 115 and (name...CB114 - 231115 - 232
173ALAALALYSLYS(chain C and (resid 114 or (resid 115 and (name...CB114 - 231115 - 232
213ALAALAASPASP(chain E and resid 114 through 228)EA114 - 228115 - 229

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Protein TOC75, chloroplastic / 75 kDa chloroplast outer envelope protein / 75 kDa translocon at the outer-envelope membrane of ...75 kDa chloroplast outer envelope protein / 75 kDa translocon at the outer-envelope membrane of chloroplasts / Import intermediate-associated protein of 75 kDa


Mass: 35527.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Gene: TOC75, IAP75, OEP75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q43715
#2: Antibody fabax9 Heavy Chain


Mass: 26466.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Antibody fabax9 Light Chain


Mass: 23596.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Sodium Hepes pH 7, 18% PEG 12,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 69080 / % possible obs: 85.9 % / Redundancy: 3 % / Biso Wilson estimate: 31.7 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rpim(I) all: 0.082 / Rrim(I) all: 0.148 / Net I/σ(I): 11.58
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Num. unique obs: 7224 / CC1/2: 0.275 / CC star: 0.657 / Rpim(I) all: 0.668 / % possible all: 88.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BJZ, 5UAY
Resolution: 2→41.66 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 1953 2.83 %
Rwork0.2109 66963 -
obs0.2122 68916 85.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.5 Å2 / Biso mean: 41.3612 Å2 / Biso min: 12 Å2
Refinement stepCycle: final / Resolution: 2→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8460 0 0 422 8882
Biso mean---39.64 -
Num. residues----1106
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1893X-RAY DIFFRACTION12.88TORSIONAL
12D1893X-RAY DIFFRACTION12.88TORSIONAL
21B1853X-RAY DIFFRACTION12.88TORSIONAL
22H1853X-RAY DIFFRACTION12.88TORSIONAL
31C1027X-RAY DIFFRACTION12.88TORSIONAL
32E1027X-RAY DIFFRACTION12.88TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.33281450.32084848499385
2.05-2.10.32831260.30164845497188
2.1-2.160.30951550.28264846500185
2.16-2.230.29491110.26454487459881
2.23-2.310.32151430.27374549469281
2.31-2.410.31441410.25465093523490
2.41-2.510.29591450.25094941508689
2.51-2.650.31531540.25184903505788
2.65-2.810.34561550.24614803495886
2.81-3.030.26491360.23264654479083
3.03-3.340.27191270.21944341446877
3.34-3.820.24511500.1874720487085
3.82-4.810.18411300.15284841497186
4.81-41.660.20271350.16385092522791
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)
10.0847-0.0432-0.0540.02280.02950.02240.05270.054-0.00880.06830.0398-0.08130.3034-0.20730.00010.2818-0.046-0.06340.40090.02340.3161-45.1322-7.372429.3872
20.03040.0184-0.02050.0242-0.05070.0379-0.10130.48490.0885-0.09490.2489-0.1247-0.08190.0977-0.03830.1478-0.040.1260.9203-0.02810.3894-26.9929-10.560715.6431
30.19260.16370.15520.2580.08740.412-0.1316-0.0764-0.119-0.14760.14480.1559-0.20420.5290.03050.2480.0794-0.05030.54730.00740.2251-32.6744-11.990525.904
40.1084-0.0632-0.24220.2316-0.04360.775-0.1186-0.08920.0789-0.1848-0.53690.64060.23260.0165-0.05170.14470.078-0.04180.4179-0.23120.4912-54.2471-6.279226.8748
50.1342-0.01420.31090.1095-0.02860.28190.05960.1459-0.046-0.3333-0.33450.3484-0.22250.2672-0.04590.33980.0599-0.08750.2765-0.08770.2994-46.08651.397422.9118
60.04030.00550.02520.0195-0.00580.06720.1865-0.2752-0.08890.1339-0.02120.2324-0.0312-0.0314-00.38330.007-0.02990.3135-0.01410.2343-40.5359-0.115427.0283
70.126-0.0371-0.01290.0272-0.00690.149-0.27830.1617-0.4045-0.03130.3502-0.2336-0.22120.0144-0.00020.30430.0711-0.0180.2362-0.03090.3207-19.7802-20.04-124.9982
80.0260.0007-0.01270.0048-0.00110.01010.1191-0.0051-0.054-0.0229-0.02390.01380.0776-0.114-0.00010.96480.07720.20660.7727-0.15420.8176-21.6833-8.719-114.4065
90.18260.0513-0.1760.0702-0.12920.3696-0.1306-0.18350.27820.4077-0.26980.3593-0.54060.1054-0.00970.62210.0559-0.01490.275-0.02010.4125-36.7881-7.2916-106.6475
100.03280.03290.00070.1992-0.12510.13730.26590.31830.14850.005-0.08090.0289-0.3697-0.41490.06010.29720.15410.00030.31070.04050.2886-34.3644-12.8776-119.1115
110.17090.0056-0.17720.02770.00280.0374-0.08940.2064-0.06960.22480.17410.12880.19050.22970.00030.28440.04760.01950.28720.05820.3037-16.9535-30.0891-123.1594
12-0.01110.0054-0.05530.3760.07971.037-0.0183-0.5346-0.307-0.03010.6421-0.241-0.04970.64390.94220.05270.2605-0.1230.39840.21240.2437-10.4145-26.334-117.4791
130.1871-0.29220.21740.4999-0.28460.2581-0.18920.3970.21490.02640.0594-0.0458-0.0888-0.0781-00.2543-0.0083-0.06210.24110.0110.2734-14.7022-19.4047-121.4495
140.53620.5438-0.48040.69060.5691.0543-0.0254-0.1435-0.01580.11390.0149-0.0091-0.0228-0.2034-0.00090.12430.02390.00760.22090.02060.2371-49.7619-27.71316.7502
15-0.1018-0.213-0.09370.6962-0.41371.5492-0.04410.01650.12380.0897-0.01390.00630.42370.0269-0.31570.0905-0.0260.03910.2154-0.02010.1738-44.6295-30.3036-2.9698
160.8294-0.11160.11950.87480.42080.45290.10730.30120.22880.3893-0.3808-0.24910.9656-0.3305-0.42470.6362-0.11850.020.122-0.09030.1513-45.54-47.2883-20.0115
170.62710.627-0.5550.71170.23351.11090.08610.02620.0045-0.0507-0.02560.09560.12520.1038-0.00360.19520.05040.01510.1468-0.03280.2716-40.6747-35.2134-102.1654
180.50330.02840.3183-0.1710.33360.9229-0.05730.1240.08860.04050.012-0.01950.1808-0.1196-0.1740.21770.03630.05490.032-0.03680.2425-43.6287-30.0418-93.8858
190.5860.0274-0.81870.5185-0.31870.5831-0.44820.08740.21320.03170.1948-0.07430.2518-0.6136-0.10430.2882-0.10030.02490.4208-0.03840.2283-60.3526-35.4014-75.5046
200.67360.0507-0.8560.4512-0.60271.93590.3941-0.3403-0.06150.2852-0.6492-0.2801-1.03720.9565-0.1080.1891-0.2138-0.01070.47790.04090.2955-30.8708-18.3434-80.8326
210.2218-0.07260.1830.25030.19740.56870.2636-0.0827-0.0641-0.0189-0.24110.1778-0.29950.20660.00040.2172-0.0433-0.0060.1910.00840.2122-35.1183-16.8474-91.5311
220.07670.0143-0.03850.1441-0.04060.03290.0235-0.35550.21660.10760.022-0.1846-0.46360.4892-0.02740.265-0.18870.01420.4021-0.00560.2713-28.2455-12.2024-89.5473
230.00720.0773-0.02070.383-0.45140.84080.2023-0.0601-0.09830.2422-0.47430.0226-0.50540.6245-0.10940.2434-0.02430.00940.2362-0.03020.2507-34.1107-21.1531-91.1019
240.03870.0646-0.00380.07850.03910.05490.1928-0.1309-0.31760.45-0.2378-0.2349-0.18630.2102-0.00190.3061-0.04490.08190.2819-0.03910.2053-41.4388-18.819-69.9308
251.3184-0.72580.35131.33460.03880.4869-0.2825-0.4040.0083-0.36360.1099-0.49280.4151-0.5468-0.15990.4081-0.18850.08580.48940.08480.0674-58.1131-40.2871-64.1205
260.10220.03270.02540.22270.270.2514-0.2369-0.55360.183-0.16350.082-0.38830.26890.38990.00340.29040.03640.01180.50410.08530.2912-45.5798-34.0515-59.3505
270.32680.3643-0.1950.25280.1570.4076-0.1355-0.2799-0.1140.0575-0.0723-0.25570.10780.08220.0020.34760.03370.04490.50390.08440.2593-49.9486-37.0418-63.8832
280.15490.2527-0.1050.3630.03160.11080.0344-0.2068-0.0840.3130.1831-0.13980.21810.30160.02420.3129-0.13050.0270.66480.01590.2161-52.8276-32.7243-54.1881
290.50080.260.03230.56770.08230.5004-0.0860.14830.2372-0.42110.30880.0993-0.85790.39460.16990.479-0.13260.03440.2583-0.03430.2003-36.2837-13.9935-14.1168
300.2689-0.08370.4416-0.0109-0.05130.7821-0.17910.1294-0.2556-0.0849-0.0530.0095-0.870.1249-0.11160.3826-0.01420.05610.1773-0.01710.2058-37.5322-12.1474-4.3706
310.13190.03450.19030.5299-0.20050.3812-0.151-0.1342-0.3049-0.34260.202-0.02230.0020.47910.05820.0974-0.05940.01390.3511-0.0190.2329-30.8817-22.7884-3.2183
320.1931-0.0127-0.08440.4960.28460.1542-0.0357-0.48670.2256-0.0345-0.27040.0967-0.78960.1888-0.25320.4074-0.84540.1308-0.796-0.00050.3225-31.1599-10.0218-5.6615
330.25370.00320.1983-0.00010.02330.13320.0981-0.06560.041-0.12860.2449-0.1199-0.53210.66470.03320.1686-0.08160.04650.2437-0.04180.2533-33.7029-20.9457-10.214
34-0.02680.09240.07010.08920.12460.1763-0.2821-0.07930.1733-0.1085-0.1065-0.0148-0.2355-0.4791-0.00010.33990.0184-0.04760.1538-0.02590.2716-44.9653-13.86334.4867
350.1537-0.08290.01660.0358-0.02970.1188-0.03110.05090.0136-0.13230.04670.0771-0.04950.33670.00730.3844-0.09610.04790.23170.00070.2055-36.8337-30.2014-28.2261
361.9036-0.85310.2673.0906-0.62940.62170.0594-0.15090.34750.0124-0.4632-0.29690.207-0.7042-0.32210.4219-0.18810.00560.4728-0.1427-0.0068-52.8771-47.245-30.1015
370.5256-0.2097-0.35810.48710.36230.34160.23270.48310.2205-0.5723-0.35670.1948-0.4184-0.27720.00480.67650.0457-0.0676-0.02550.02610.3574-44.9632-31.0701-33.7799
380.23930.24540.07540.16030.10380.1540.06350.07350.4323-0.1077-0.38690.451-0.0875-0.2166-0.01040.47280.0982-0.13460.3355-0.110.3196-55.298-34.7467-34.7823
390.02440.01460.00790.00990.0071-0.00120.3321-0.3766-0.32790.48040.0417-0.06870.77010.1581-0.00010.40520.0460.05330.21690.02880.2625-35.0717-31.6651-22.4907
400.1668-0.2190.02590.25060.0118-0.037-0.2437-0.25820.359-0.3774-0.22410.20570.3532-0.6194-0.05390.4186-0.1445-0.05270.5159-0.08890.2407-58.166-43.4173-35.0194
410.376-0.2358-0.26610.15270.17380.22610.01930.1627-0.061-0.2723-0.0643-0.0026-0.1913-0.3371-0.03140.6847-0.0467-0.02780.29390.02820.2314-46.3372-39.3578-40.8753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 113 through 121 )E113 - 121
2X-RAY DIFFRACTION2chain 'E' and (resid 122 through 138 )E122 - 138
3X-RAY DIFFRACTION3chain 'E' and (resid 139 through 166 )E139 - 166
4X-RAY DIFFRACTION4chain 'E' and (resid 167 through 184 )E167 - 184
5X-RAY DIFFRACTION5chain 'E' and (resid 185 through 218 )E185 - 218
6X-RAY DIFFRACTION6chain 'E' and (resid 219 through 228 )E219 - 228
7X-RAY DIFFRACTION7chain 'C' and (resid 114 through 126 )C114 - 126
8X-RAY DIFFRACTION8chain 'C' and (resid 127 through 131 )C127 - 131
9X-RAY DIFFRACTION9chain 'C' and (resid 132 through 138 )C132 - 138
10X-RAY DIFFRACTION10chain 'C' and (resid 139 through 159 )C139 - 159
11X-RAY DIFFRACTION11chain 'C' and (resid 160 through 184 )C160 - 184
12X-RAY DIFFRACTION12chain 'C' and (resid 185 through 202 )C185 - 202
13X-RAY DIFFRACTION13chain 'C' and (resid 203 through 231 )C203 - 231
14X-RAY DIFFRACTION14chain 'D' and (resid 5 through 102 )D5 - 102
15X-RAY DIFFRACTION15chain 'D' and (resid 103 through 150 )D103 - 150
16X-RAY DIFFRACTION16chain 'D' and (resid 151 through 232 )D151 - 232
17X-RAY DIFFRACTION17chain 'A' and (resid 4 through 94 )A4 - 94
18X-RAY DIFFRACTION18chain 'A' and (resid 95 through 150 )A95 - 150
19X-RAY DIFFRACTION19chain 'A' and (resid 151 through 231 )A151 - 231
20X-RAY DIFFRACTION20chain 'B' and (resid 3 through 19 )B3 - 19
21X-RAY DIFFRACTION21chain 'B' and (resid 20 through 62 )B20 - 62
22X-RAY DIFFRACTION22chain 'B' and (resid 63 through 76 )B63 - 76
23X-RAY DIFFRACTION23chain 'B' and (resid 77 through 104 )B77 - 104
24X-RAY DIFFRACTION24chain 'B' and (resid 105 through 116 )B105 - 116
25X-RAY DIFFRACTION25chain 'B' and (resid 117 through 140 )B117 - 140
26X-RAY DIFFRACTION26chain 'B' and (resid 141 through 158 )B141 - 158
27X-RAY DIFFRACTION27chain 'B' and (resid 159 through 200 )B159 - 200
28X-RAY DIFFRACTION28chain 'B' and (resid 201 through 216 )B201 - 216
29X-RAY DIFFRACTION29chain 'H' and (resid 3 through 19 )H3 - 19
30X-RAY DIFFRACTION30chain 'H' and (resid 20 through 39 )H20 - 39
31X-RAY DIFFRACTION31chain 'H' and (resid 40 through 62 )H40 - 62
32X-RAY DIFFRACTION32chain 'H' and (resid 63 through 76 )H63 - 76
33X-RAY DIFFRACTION33chain 'H' and (resid 77 through 92 )H77 - 92
34X-RAY DIFFRACTION34chain 'H' and (resid 93 through 104 )H93 - 104
35X-RAY DIFFRACTION35chain 'H' and (resid 105 through 121 )H105 - 121
36X-RAY DIFFRACTION36chain 'H' and (resid 122 through 140 )H122 - 140
37X-RAY DIFFRACTION37chain 'H' and (resid 141 through 153 )H141 - 153
38X-RAY DIFFRACTION38chain 'H' and (resid 154 through 166 )H154 - 166
39X-RAY DIFFRACTION39chain 'H' and (resid 167 through 177 )H167 - 177
40X-RAY DIFFRACTION40chain 'H' and (resid 178 through 193 )H178 - 193
41X-RAY DIFFRACTION41chain 'H' and (resid 194 through 217 )H194 - 217

+
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