[English] 日本語
Yorodumi
- PDB-6iap: structure of human NKp46 in complex with antibody NKp46-1 and NKp46-4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6iap
Titlestructure of human NKp46 in complex with antibody NKp46-1 and NKp46-4
Components
  • Fab NKp46-1 heavy chain
  • Fab NKp46-1 light chain
  • Fab NKp46-4 heavy chain
  • Fab NKp46-4 light chain
  • Natural cytotoxicity triggering receptor 1
KeywordsIMMUNE SYSTEM / THERAPEUTIC ANTIBODY
Function / homology
Function and homology information


regulation of natural killer cell mediated cytotoxicity / immune response-regulating signaling pathway / natural killer cell activation / SWI/SNF complex / cellular defense response / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signal transduction / plasma membrane
Similarity search - Function
: / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Natural cytotoxicity triggering receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsRoussel, A. / Amigues, B.
CitationJournal: Cell / Year: 2019
Title: Multifunctional Natural Killer Cell Engagers Targeting NKp46 Trigger Protective Tumor Immunity.
Authors: Gauthier, L. / Morel, A. / Anceriz, N. / Rossi, B. / Blanchard-Alvarez, A. / Grondin, G. / Trichard, S. / Cesari, C. / Sapet, M. / Bosco, F. / Rispaud-Blanc, H. / Guillot, F. / Cornen, S. / ...Authors: Gauthier, L. / Morel, A. / Anceriz, N. / Rossi, B. / Blanchard-Alvarez, A. / Grondin, G. / Trichard, S. / Cesari, C. / Sapet, M. / Bosco, F. / Rispaud-Blanc, H. / Guillot, F. / Cornen, S. / Roussel, A. / Amigues, B. / Habif, G. / Caraguel, F. / Arrufat, S. / Remark, R. / Romagne, F. / Morel, Y. / Narni-Mancinelli, E. / Vivier, E.
History
DepositionNov 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev / database_PDB_rev_record
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Natural cytotoxicity triggering receptor 1
D: Fab NKp46-4 light chain
E: Fab NKp46-4 heavy chain
H: Fab NKp46-1 heavy chain
L: Fab NKp46-1 light chain


Theoretical massNumber of molelcules
Total (without water)113,7265
Polymers113,7265
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10120 Å2
ΔGint-58 kcal/mol
Surface area45190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.858, 73.827, 128.518
Angle α, β, γ (deg.)90.000, 90.570, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Antibody , 4 types, 4 molecules DEHL

#2: Antibody Fab NKp46-4 light chain


Mass: 23056.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab NKp46-4 heavy chain


Mass: 23192.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody Fab NKp46-1 heavy chain


Mass: 23521.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)
#5: Antibody Fab NKp46-1 light chain


Mass: 23244.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)

-
Protein / Non-polymers , 2 types, 160 molecules A

#1: Protein Natural cytotoxicity triggering receptor 1 / Lymphocyte antigen 94 homolog / NK cell-activating receptor / Natural killer cell p46-related protein / hNKp46


Mass: 20710.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCR1, LY94 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O76036
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M acid carboxylique, 0.1M Tris/bicine pH8.5, 50%P500MME/P20k

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.89→48.47 Å / Num. obs: 28415 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 81.39 Å2 / Net I/σ(I): 5.2
Reflection shellResolution: 2.89→3.05 Å / Num. unique obs: 28397

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OLL

1oll


Resolution: 2.9→48.47 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.399
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1399 4.93 %RANDOM
Rwork0.187 ---
obs0.191 28397 99.3 %-
Displacement parametersBiso max: 212.29 Å2 / Biso mean: 91.8 Å2 / Biso min: 44.45 Å2
Baniso -1Baniso -2Baniso -3
1--9.6439 Å20 Å2-22.2483 Å2
2--14.344 Å20 Å2
3----4.7001 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.9→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7979 0 0 159 8138
Biso mean---74.92 -
Num. residues----1041
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2695SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1363HARMONIC5
X-RAY DIFFRACTIONt_it8190HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1080SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8998SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8190HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11150HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion21.07
LS refinement shellResolution: 2.9→2.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3792 31 5.46 %
Rwork0.2443 537 -
all0.251 568 -
obs--86.47 %
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)
1-0.05760.11632.896803.33190.05760.0047-0.0877-0.221-0.23580.03180.13770.0472-0.1063-0.03650.02230.01020.0534-0.07830.1376-0.13417.306111.5582-24.6528
20.05961.1875-3.00675.21491.93322.06090.01380.2385-0.05830.1134-0.0143-0.12140.2666-0.11280.00050.3806-0.02350.1397-0.11080.06840.014923.715610.6953-30.0721
35.43652.7981-2.71264.0758-9.16718.87810.05060.1338-0.0450.09340.05920.12150.1054-0.0648-0.10980.03890.3249-0.07080.09470.25850.073730.163510.1346-33.216
41.50493.258-1.1213.7385-0.45737.4245-0.0396-0.1563-0.11080.0088-0.028-0.2120.07220.24450.06760.12380.0997-0.0017-0.14770.1431-0.012425.737110.1794-23.8782
5-0.02210.43421.1080.60392.30110.85190.0045-0.0299-0.2380.22760.0180.00850.0516-0.2464-0.02250.24910.02590.0278-0.19310.0931-0.135123.028615.6766-37.7103
60.0159-1.8664-0.34741.58562.136-0.00690.0386-0.2994-0.11390.10960.06010.2545-0.1559-0.5807-0.0987-0.05850.05720.14770.24810.2648-0.04456.512620.8055-5.4622
70.6096-1.05581.4781.72861.71220.0293-0.0374-0.2552-0.04920.33360.052-0.0728-0.268-0.2408-0.01460.00470.04740.05520.09220.0158-0.27610.127825.6382-4.8689
88.10121.49560.83030-7.79913.07820.0751-0.0068-0.3945-0.06150.05150.12820.303-0.0852-0.12650.07990.14090.04910.09030.24880.00935.404623.7538-9.7241
92.692-2.3059-0.6090-0.8647-0.0124-0.01640.02320.0373-0.20140.07410.24510.0833-0.1002-0.0577-0.06950.0349-0.00210.10090.32140.2726-1.460517.3105-7.6911
102.3657-4.39552.81521.2737-2.75180.0558-0.0316-0.0826-0.0577-0.29020.01360.0651-0.1064-0.14030.0180.09020.04270.0798-0.07770.1734-0.227115.525620.6194-7.1019
111.5036-0.2727-4.19494.4224-0.00675.7427-0.212-0.1891-0.37140.23260.1887-0.27810.28570.03620.02330.31530.13530.03610.0664-0.0240.195844.94134.2691-54.7822
121.46690.0418-1.97626.67462.00717.3087-0.10980.1988-0.1495-0.06920.0040.34190.0188-0.09530.10580.0512-0.03370.0755-0.1977-0.0564-0.05435.52510.5746-60.3773
133.7988-0.127-3.35963.69073.47245.9304-0.03790.0586-0.2070.21530.0931-0.07340.1787-0.1375-0.05520.16260.00570.1184-0.44470.0632-0.060840.25587.1554-57.8207
142.0067-2.4062-0.49775.29622.6967-0.0101-0.0455-0.1972-0.09720.18770.135-0.1771-0.02880.104-0.08950.0196-0.0762-0.0416-0.0735-0.02970.094649.178610.9705-61.5552
150.46392.88683.94210.5216.13850.07840.0569-0.20070.2808-0.0789-0.0167-0.2334-0.25650.3695-0.0402-0.057-0.18720.1057-0.2874-0.1220.064468.892428.9962-72.406
16-0.09820.19474.9291.4680.5680.8550.0463-0.1351-0.0522-0.08980.0727-0.00770.16240.3652-0.1189-0.1635-0.00670.06030.1019-0.09910.052474.370619.938-65.0449
17-0.0041.22531.38182.0764-2.70750.0275-0.0193-0.10160.0206-0.08130.02190.03230.12910.1759-0.00260.1898-0.29090.06110.0267-0.12450.006769.114525.3938-60.5614
180.25011.4975-0.83895.62330.8202-0.01670.1268-0.21420.175-0.14160.1018-0.0624-0.29620.2912-0.2286-0.0117-0.06590.1052-0.1833-0.13290.057364.112425.0413-69.1708
192.05082.1143-0.78090.6018-4.86650.09930.0603-0.07010.1616-0.0840.0917-0.11140.2570.2107-0.15190.0256-0.18530.15660.0705-0.14390.213979.057326.0736-68.3886
202.3551-0.4229-2.07870-4.00610.13370.0621-0.0592-0.0714-0.08280.0665-0.0791-0.12090.3558-0.1286-0.0222-0.02090.1027-0.1472-0.08190.163876.61319.8594-73.7506
210.0365-0.9997-1.83491.10332.3429-0.03650.0190.05350.1066-0.23610.11170.110.1266-0.245-0.13070.14190.03120.0249-0.19940.0874-0.107433.355731.0957-57.5096
223.9623-0.3919-1.71017.59780.1264.59280.0024-0.34510.1211-0.09620.2027-0.2656-0.20150.5178-0.20520.13330.00820.0278-0.2208-0.0649-0.223236.334429.2095-49.6314
23-0.0124-1.78650.60376.1512-0.07193.5639-0.03080.015-0.07460.2939-0.0450.1317-0.05310.09790.07580.0119-0.0084-0.0638-0.1355-0.0096-0.111535.221922.5305-42.5918
240.2871-1.1785-1.08030.13941.3498-0.01590.0118-0.1450.00910.11330.01850.0349-0.01590.0415-0.03030.1037-0.0414-0.10830.3704-0.04660.112744.424824.9069-37.3383
250.09772.8947-4.9261.29690.76412.8690.0212-0.12810.1659-0.19110.16130.0729-0.1330.137-0.18250.05160.03170.0811-0.2149-0.0958-0.013437.244332.5254-44.1582
264.4595-0.3088-1.95191.348-1.11133.41090.0305-0.220.3238-0.3140.074-0.2956-0.16450.0398-0.10450.2544-0.06630.1165-0.376-0.15460.124951.291729.6755-62.8216
273.0712-2.0591.18760.5326-3.26812.85280.2084-0.28980.6122-0.4443-0.16650.0967-0.0216-0.1747-0.04190.0839-0.15190.1376-0.2407-0.23020.257654.581635.1697-71.0964
2812.47642.8584-4.73318.181-1.9557-0.05990.05840.03780.1854-0.1786-0.0514-0.109-0.07910.0924-0.0070.0319-0.02630.0904-0.3254-0.08310.076261.027730.9806-72.1814
290.0589-0.4097-2.96142.9175-3.48410.6866-0.02020.0590.2668-0.1401-0.0537-0.009-0.0765-0.0340.07390.1362-0.03970.3189-0.2978-0.19080.351654.202541.3312-73.614
300.0365-0.0324-1.83520.8183-0.61260.0006-0.01070.0616-0.0128-0.0541-0.0091-0.0075-0.00610.07370.01980.3398-0.06510.0801-0.37350.06570.038964.758741.0367-80.4029
310.02040.53690.61920.4895-3.26282.0718-0.00510.166-0.1114-0.0308-0.0849-0.03180.0537-0.00490.09-0.0224-0.0206-0.12-0.01390.0097-0.100741.749515.840.7927
320.7022-0.0251-0.11940.416-1.17370.7679-0.00120.05720.0320.0222-0.00590.0062-0.1042-0.11780.00710.2816-0.0906-0.0402-0.0634-0.03490.150251.780833.33411.6322
331.965-3.1101-0.99280.5741-1.9112-0.01990.02950.20310.0306-0.3081-0.05320.1154-0.2675-0.09480.02370.09210.02950.0297-0.11380.0307-0.174236.931122.144-1.5752
342.43045.2066-2.23272.0906-0.7827-0.0447-0.0162-0.351-0.02440.10360.03520.0045-0.12520.1123-0.0190.02710.1294-0.18840.0484-0.1653-0.171935.744825.700314.7049
350.9043-1.994-2.41994.63790.4277-0.0482-0.0364-0.01650.47730.03160.14130.0525-0.2904-0.1605-0.10490.20410.1427-0.1222-0.2054-0.07390.059232.018632.30913.4745
362.36941.81782.00090.0154-1.30790.0396-0.0884-0.16340.27120.18150.0924-0.3008-0.4756-0.0094-0.00390.11540.02290.061-0.1645-0.0635-0.132538.174126.10255.9123
371.9631-2.12150.0761.9792-0.96135.5040.0273-0.09540.0796-0.3314-0.0621-0.257-0.5601-0.17170.03480.13450.06660.0447-0.20940.06980.045344.972421.907611.4173
388.93140.516-0.94778.08537.76665.4761-0.13720.3233-0.2697-0.00010.2187-0.02820.30750.2982-0.0815-0.0766-0.17290.11760.0587-0.1018-0.27862.37628.023824.0557
395.10330.87222.37174.34970.05355.65860.11030.412-0.2142-0.1693-0.05990.12740.16950.2528-0.0505-0.0711-0.11590.0386-0.0436-0.0305-0.141157.55127.817119.9187
402.98693.26361.54420.0141-0.53063.22780.03710.20520.2449-0.11680.12270.0379-0.07180.2903-0.15990.0869-0.1330.27440.0714-0.0567-0.211663.55759.547912.7523
410.0348-3.4849-1.75160.83832.51110.13240.0885-0.40190.14820.0858-0.20430.0151-0.4253-0.10410.1157-0.1583-0.00320.10750.17-0.0403-0.197126.989815.092525.5933
427.99723.8016-6.13193.72742.03716.77850.0771-0.1702-0.09280.2082-0.2050.03330.096-0.34480.12790.03030.0910.13940.6778-0.0163-0.060419.678914.556919.9062
430.20242.5486-0.75973.3705-4.85213.0777-0.0588-0.19520.06740.07990.0738-0.1664-0.0154-0.0041-0.0151-0.1512-0.0755-0.02310.2046-0.003-0.207432.12411.260513.8071
445.6864.17413.29542.8884-6.49420.68420.078-0.3896-0.23980.15080.10160.10360.2452-0.31-0.1795-0.0895-0.06220.09290.19440.0572-0.064621.06638.464913.9444
451.38160.61691.92755.9195-0.53735.60190.0458-0.2946-0.08840.0454-0.1666-0.0332-0.3592-0.66610.1208-0.1427-0.02950.17690.1590.0718-0.293428.134213.048218.4542
460.0253-2.7292-1.28471.1927-0.60263.01160.0151-0.0088-0.1356-0.30820.14750.00310.15630.1259-0.16260.0314-0.0906-0.04040.0038-0.0551-0.130254.56062.860130.948
471.5576-0.45874.34621.071.22586.30250.0110.1226-0.0243-0.14410.19540.0970.08870.0043-0.2064-0.0108-0.03330.1199-0.14770.01370.004759.223410.011635.6844
480.2445-0.1669-2.37433.19120.61722.1467-0.0546-0.07410.265-0.14440.2722-0.03140.2183-0.2681-0.21760.0105-0.09010.05280.05380.02270.01348.8718.313628.3335
495.10991.6993-1.45371.49930.8923.52630.022-0.03280.05370.02810.1081-0.096-0.06640.2621-0.1301-0.0358-0.0256-0.06480.02620.09420.031961.54159.423837.3807
500.02651.5226-1.33070-4.112-0.0265-0.00320.04110.0246-0.12170.0142-0.0905-0.12760.1545-0.0111-0.21980.0495-0.0151-0.0011-0.0352-0.116466.08163.854439.4778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - 18 }A1 - 18
2X-RAY DIFFRACTION2{ A|19 - 39 }A19 - 39
3X-RAY DIFFRACTION3{ A|40 - 51 }A40 - 51
4X-RAY DIFFRACTION4{ A|52 - 71 }A52 - 71
5X-RAY DIFFRACTION5{ A|72 - 87 }A72 - 87
6X-RAY DIFFRACTION6{ A|88 - 117 }A88 - 117
7X-RAY DIFFRACTION7{ A|118 - 133 }A118 - 133
8X-RAY DIFFRACTION8{ A|134 - 153 }A134 - 153
9X-RAY DIFFRACTION9{ A|154 - 167 }A154 - 167
10X-RAY DIFFRACTION10{ A|168 - 182 }A168 - 182
11X-RAY DIFFRACTION11{ D|1 - 31 }D1 - 31
12X-RAY DIFFRACTION12{ D|32 - 65 }D32 - 65
13X-RAY DIFFRACTION13{ D|66 - 94 }D66 - 94
14X-RAY DIFFRACTION14{ D|95 - 110 }D95 - 110
15X-RAY DIFFRACTION15{ D|111 - 140 }D111 - 140
16X-RAY DIFFRACTION16{ D|141 - 155 }D141 - 155
17X-RAY DIFFRACTION17{ D|156 - 162 }D156 - 162
18X-RAY DIFFRACTION18{ D|163 - 186 }D163 - 186
19X-RAY DIFFRACTION19{ D|187 - 198 }D187 - 198
20X-RAY DIFFRACTION20{ D|199 - 211 }D199 - 211
21X-RAY DIFFRACTION21{ E|1 - 10 }E1 - 10
22X-RAY DIFFRACTION22{ E|11 - 42 }E11 - 42
23X-RAY DIFFRACTION23{ E|43 - 61 }E43 - 61
24X-RAY DIFFRACTION24{ E|62 - 67 }E62 - 67
25X-RAY DIFFRACTION25{ E|68 - 89 }E68 - 89
26X-RAY DIFFRACTION26{ E|90 - 146 }E90 - 146
27X-RAY DIFFRACTION27{ E|147 - 166 }E147 - 166
28X-RAY DIFFRACTION28{ E|167 - 195 }E167 - 195
29X-RAY DIFFRACTION29{ E|196 - 212 }E196 - 212
30X-RAY DIFFRACTION30{ E|213 - 217 }E213 - 217
31X-RAY DIFFRACTION31{ H|1 - 8 }H1 - 8
32X-RAY DIFFRACTION32{ H|9 - 16 }H9 - 16
33X-RAY DIFFRACTION33{ H|17 - 35 }H17 - 35
34X-RAY DIFFRACTION34{ H|36 - 49 }H36 - 49
35X-RAY DIFFRACTION35{ H|50 - 73 }H50 - 73
36X-RAY DIFFRACTION36{ H|74 - 103 }H74 - 103
37X-RAY DIFFRACTION37{ H|104 - 128 }H104 - 128
38X-RAY DIFFRACTION38{ H|129 - 155 }H129 - 155
39X-RAY DIFFRACTION39{ H|156 - 198 }H156 - 198
40X-RAY DIFFRACTION40{ H|199 - 220 }H199 - 220
41X-RAY DIFFRACTION41{ L|1 - 15 }L1 - 15
42X-RAY DIFFRACTION42{ L|16 - 34 }L16 - 34
43X-RAY DIFFRACTION43{ L|35 - 49 }L35 - 49
44X-RAY DIFFRACTION44{ L|50 - 71 }L50 - 71
45X-RAY DIFFRACTION45{ L|72 - 104 }L72 - 104
46X-RAY DIFFRACTION46{ L|105 - 123 }L105 - 123
47X-RAY DIFFRACTION47{ L|124 - 156 }L124 - 156
48X-RAY DIFFRACTION48{ L|157 - 171 }L157 - 171
49X-RAY DIFFRACTION49{ L|172 - 203 }L172 - 203
50X-RAY DIFFRACTION50{ L|204 - 211 }L204 - 211

+
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