[English] 日本語
Yorodumi
- PDB-6jpv: Structural analysis of AIMP2-DX2 and HSP70 interaction -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jpv
TitleStructural analysis of AIMP2-DX2 and HSP70 interaction
ComponentsHeat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
KeywordsCHAPERONE / HSP70 / AIMP2-DX2 / substrate binding domain
Function / homology
Function and homology information


type II pneumocyte differentiation / positive regulation of endoribonuclease activity / denatured protein binding / Selenoamino acid metabolism / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding ...type II pneumocyte differentiation / positive regulation of endoribonuclease activity / denatured protein binding / Selenoamino acid metabolism / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / Cytosolic tRNA aminoacylation / misfolded protein binding / regulation of mitotic spindle assembly / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / aminoacyl-tRNA synthetase multienzyme complex / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / regulation of protein ubiquitination / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chaperone-mediated protein complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / protein folding chaperone / inclusion body / negative regulation of protein ubiquitination / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / positive regulation of protein ubiquitination / AUF1 (hnRNP D0) binds and destabilizes mRNA / positive regulation of interleukin-8 production / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / virus receptor activity / positive regulation of NF-kappaB transcription factor activity / cellular response to heat / cellular response to oxidative stress / protein refolding / protein-containing complex assembly / vesicle / ficolin-1-rich granule lumen / molecular adaptor activity / receptor ligand activity / blood microparticle / protein stabilization / protein ubiquitination / nuclear speck / ribonucleoprotein complex / cadherin binding / translation / negative regulation of cell population proliferation / focal adhesion / signaling receptor binding / centrosome / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
AIMP2, lysyl-tRNA synthetase binding domain / AIMP2, thioredoxin-like domain / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / AIMP2 lysyl-tRNA synthetase binding domain / Thioredoxin-like domain / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily ...AIMP2, lysyl-tRNA synthetase binding domain / AIMP2, thioredoxin-like domain / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / AIMP2 lysyl-tRNA synthetase binding domain / Thioredoxin-like domain / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal domain superfamily / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Heat shock 70 kDa protein 1A / Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15000649024 Å
AuthorsCho, H.Y. / Son, S.Y. / Jeon, Y.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2013M3A6A4045160 Korea, Republic Of
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Targeting the interaction of AIMP2-DX2 with HSP70 suppresses cancer development.
Authors: Lim, S. / Cho, H.Y. / Kim, D.G. / Roh, Y. / Son, S.Y. / Mushtaq, A.U. / Kim, M. / Bhattarai, D. / Sivaraman, A. / Lee, Y. / Lee, J. / Yang, W.S. / Kim, H.K. / Kim, M.H. / Lee, K. / Jeon, Y.H. / Kim, S.
History
DepositionMar 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Dec 18, 2019Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
Revision 1.3Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.4Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
B: Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2


Theoretical massNumber of molelcules
Total (without water)33,7382
Polymers33,7382
Non-polymers00
Water5,963331
1
A: Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2

B: Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2


Theoretical massNumber of molelcules
Total (without water)33,7382
Polymers33,7382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area3130 Å2
ΔGint-20 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.111, 77.054, 88.711
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLU(chain 'A' and (resid 394 through 534 or resid 536 through 545))AA394 - 5341 - 141
12VALVALHISHIS(chain 'A' and (resid 394 through 534 or resid 536 through 545))AA536 - 545143 - 152
21SERSERGLUGLU(chain 'B' and (resid 394 through 534 or resid 536 through 545))BB394 - 5341 - 141
22VALVALHISHIS(chain 'B' and (resid 394 through 534 or resid 536 through 545))BB536 - 545143 - 152

-
Components

#1: Protein Heat shock 70 kDa protein 1A,Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 / Heat shock 70 kDa protein 1 / HSP70.1 / Multisynthase complex auxiliary component p38 / Protein JTV-1


Mass: 16869.021 Da / Num. of mol.: 2
Fragment: HSP70 substrate binding domain/peptide sequences of DX2
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs.,SF file contains Friedel pairs.
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSP72, HSPA1, HSX70, AIMP2, JTV1, PRO0992 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: P0DMV8, UniProt: Q13155
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSubstrate binding domain of HSP70: S394-S537 Peptide from AIMP2-DX2: M538-G546

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG1500, Succinic Acid, Sodium Dihydrogen Phosphate, Glycine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2018
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→28.08 Å / Num. obs: 15918 / % possible obs: 99.72 % / Redundancy: 7.7 % / Biso Wilson estimate: 18.93 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1036 / Rpim(I) all: 0.04137 / Rrim(I) all: 0.1118 / Net I/σ(I): 14.26
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 8 % / Rmerge(I) obs: 0.2348 / Mean I/σ(I) obs: 8.73 / Num. unique obs: 1551 / CC1/2: 0.97 / Rpim(I) all: 0.08955 / Rrim(I) all: 0.2517 / % possible all: 99.87

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.12_2829phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WV5
Resolution: 2.15000649024→28.0785408959 Å / SU ML: 0.257560777566 / Cross valid method: FREE R-VALUE / σ(F): 1.35779936231 / Phase error: 22.9145895941
RfactorNum. reflection% reflectionSelection details
Rfree0.23478720108 2154 7.69203299646 %Random selection
Rwork0.173762231727 ---
obs0.17847200903 15894 94.6239102521 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.3642749192 Å2
Refinement stepCycle: LAST / Resolution: 2.15000649024→28.0785408959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 0 331 2690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006880919159852398
X-RAY DIFFRACTIONf_angle_d0.9575778231763244
X-RAY DIFFRACTIONf_chiral_restr0.0559951226453377
X-RAY DIFFRACTIONf_plane_restr0.00582881842173430
X-RAY DIFFRACTIONf_dihedral_angle_d18.19063440421501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.2638592076221120.1822787155151323X-RAY DIFFRACTION73.4390992835
2.2-2.2550.2330753598281190.1936072986461457X-RAY DIFFRACTION79.5557799091
2.255-2.31590.2572158287831270.1889482890321584X-RAY DIFFRACTION86.7647058824
2.3159-2.38410.269949248481460.1784277243471675X-RAY DIFFRACTION91.5075376884
2.3841-2.4610.2992541412351410.1913281428491745X-RAY DIFFRACTION96.0774325013
2.461-2.54890.3111983364151520.1904684523571797X-RAY DIFFRACTION98.6835443038
2.5489-2.65080.2937042448871510.1860061541931813X-RAY DIFFRACTION99.8982706002
2.6508-2.77140.2810013494941520.1844138668521820X-RAY DIFFRACTION99.8481012658
2.7714-2.91740.2314381537151520.1890999160771828X-RAY DIFFRACTION99.8487140696
2.9174-3.09990.25534646581530.1831940920211814X-RAY DIFFRACTION99.6958945768
3.0999-3.33890.2144666234521520.1685701991271799X-RAY DIFFRACTION99.2370295015
3.3389-3.67430.2183056406821450.1540161847741822X-RAY DIFFRACTION99.2431886983
3.6743-4.20440.1854949306331490.1502899391121802X-RAY DIFFRACTION99.3380855397
4.2044-5.29130.1892164266871520.1476471215971792X-RAY DIFFRACTION98.9816700611
5.2913-28.08090.2225312818481510.1940991122191778X-RAY DIFFRACTION97.5227502528
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)
11.77884450176-0.814271882398-1.490756458856.292562516384.080035419714.67381333651-0.0987149500286-0.00683156194868-0.0896445824362-0.0347879359709-0.3025509909320.7295034321970.133280704096-0.3206402846370.302533628610.0977832294423-0.0294161600288-0.0001530643225580.14901121680.01849735246230.165118260552-9.47613986407-9.21916932182110.289183073
21.17345392268-0.305918440722-2.253720429021.034395613421.685401939615.599530809890.07241228911680.0266598111335-0.0745040798497-0.342033903966-0.2880746083110.670578568938-0.660957912907-1.488961457460.2793251324430.1949265590840.128177404506-0.06311492887530.6383256599130.05753026240410.472455623529-14.3421544748-6.73347803518106.838925159
33.561505535231.06778420168-3.517954830195.199063643520.8492654030234.21329068817-0.6754623017921.697514456210.166110689918-0.6097150755820.42834827365-0.08320254854460.486205878661-0.45414135640.4933694722390.8644399520410.295812686151-0.04667470051830.899263913653-0.04003958401760.383029070793-0.734238492554-16.099231069190.2586945679
48.369080204195.305474114585.932947874874.063807717883.999303872554.280797126640.283634163781.23336142320.299482666944-0.239393665811.04137497018-0.469513973481-0.04341257127121.0286526108-0.9542607062630.5678879700360.1376184658130.1645476867270.7275811610510.05680205739960.51020421789413.4762757764-18.829503005196.9927160983
58.75390201988-5.97351033716-5.929871674818.868962006155.727417927584.819913255470.00906354250828-0.4104204147850.3715938968690.2344610403810.0908829210534-0.5946504997790.5875376362890.181936761256-0.05744725401850.255669551156-0.0484430199625-0.02716305829250.31968671754-0.03085149304160.17038036578115.5675129127-11.2004919429112.851964662
68.710468159112.54283610811-1.278486460415.701230332844.997613998728.22375864613-0.598122673266-0.1851466186730.594461823774-0.7370933313960.01750312017080.815634078019-0.9893820304310.3989389096120.4108485345390.366272220730.0189392897379-0.09839864212190.292354360042-0.05241079698530.16543687664110.78228899361.96211975939127.547342205
73.4100109347-3.56240701289-2.44669710624.537660531383.99888601755.64189643967-0.01488511076710.08351384129120.4164626693360.01863388528570.0606289508288-0.189160628909-0.04947195645950.181263060802-0.03851727577330.133239304771-0.0153684641899-0.01234042819060.1232766634320.002318452701520.10523316369311.566804680911.613861821896.0099593298
81.631559387450.137740066932-0.09464477862694.423950991172.636671102884.01276115093-0.05229407237230.211464841984-0.107571833362-0.06247060035470.01736728880540.276573172852-0.1055820823080.06511069721950.06719114731090.06142944729170.0121633336935-0.006068716193810.1178518850440.0002088469572360.0935777883785.865408172582.3656202133883.0539226477
94.675019449913.007332487622.556876238142.850792445421.158698046983.040713816260.104849429188-0.105033928004-0.229005056706-0.0836357970373-0.0767180596296-0.234393692394-0.1433406054630.239869124610.03030983725920.0901217030703-0.002814117466060.02105258000610.1325998000270.01663055572330.11332948166615.95442525092.5001666305993.8569495101
102.891678218972.798042070982.078327566694.357188850832.815806024992.19892350602-0.1118457313260.0594788019499-0.5096937398730.2694650023660.284461388701-0.1708705461640.1164953132140.260859699925-0.3809391855390.108000767085-0.0304159877245-0.01461677211740.193401496653-0.02466840717920.1221330874597.54173131829-3.0460050512594.9518724133
111.81251207232-0.12699012935-0.5803296104031.645676742010.306420026343.514770473170.01625327006250.1070906083580.003706881777550.0369631903003-0.1599472653290.0508954442538-0.193896434124-0.5467328307040.02539620968590.0590618479517-0.02223974739920.0053789971330.09254336229070.004012965497560.1351830834711.735051813353.4516307575688.3962439564
125.745329401511.563903584032.857743568043.016855441540.7242179789096.72592192530.141177307252-0.2216026262240.1924417474280.551101286884-0.17871520333-0.0945253612680.01361418001340.303026225911-0.0532920624460.154457120571-0.0209792559497-0.002600291324430.114652592147-0.01288757187970.1448604523752.956682880372.3431699746898.5268498779
135.60074340953-2.93702121982-4.807538970125.053018415931.36658539267.5961784850.266980974996-1.274183570850.4179679510091.371319228060.083979538469-0.5982808434160.9060789584840.762574534553-0.2735142759610.499189425933-0.123371942-0.1403916071630.493666487733-0.0359823355280.29565312225923.701946343311.4508592633104.489663099
148.63240079007-0.211039031641.646061313769.329629940953.406721536566.655342494830.03476800388150.5513018728780.347710355023-0.530003005218-0.175246298232-0.8792814372350.1067338557770.8064387478810.0672037618680.255009338947-0.05053370063030.02229321862070.4342215623150.0417904341490.21493367930426.69662889939.5075000405587.2030962864
153.157101231941.71385326709-0.118919330935.041340643692.055890299943.203935616730.369360004177-0.5345871012140.1559256280440.8511533370450.275591175155-0.008604977081440.5011528211080.293453717330.2854172185760.1188175000210.0675629450278-0.1693135500450.157393894830.08663794297970.11863087092422.52624715441.1152643465468.8849722161
162.603883941190.1071076299470.7002526196196.22398348744.134239939514.790483334390.07374070930250.04968255559160.0211203312025-0.538946275458-0.1145844669030.107502346232-0.192786030336-0.04361352665290.02174444005060.07589084243430.01421839971050.001048554330230.07514206004880.001992812400540.08340105881511.79462589867-15.8559167453104.766431821
170.233805609147-0.09010812043340.8534066077335.154039054160.3912627421323.358433214420.242730426338-0.20593157520.035484977542-0.260030178769-0.251900289660.03058929127540.4998970745790.1246415912640.002886140697240.09139044976370.008547058577930.00983361063920.153059023758-0.01736830256330.155271704711.54096774952-19.7526573897106.833054591
181.79768756089-1.07785501539-0.704694916342.822542472541.107592600573.431013985730.0648593315286-0.03162338085280.05204356819390.03315652553470.0377507663244-0.0178466394589-0.09907995280240.143220790861-0.1034868700720.0459484391155-0.03258354501390.02741715578170.106781056602-0.01196553210360.134743065596-4.23003737175-5.64022423462111.495639434
193.1406899662-1.37428096051-1.266837301842.278122257231.008563498273.389401842320.09955570473670.1396780613090.200375684187-0.2030890569080.0304791519998-0.261440660149-0.347898930317-0.16329267417-0.06995231615950.1190755209820.00431262264490.03682925551350.1469362802690.02877079051880.08135988457842.5454626425-6.8094734179102.988823351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 463 through 492 )
2X-RAY DIFFRACTION2chain 'B' and (resid 493 through 503 )
3X-RAY DIFFRACTION3chain 'B' and (resid 504 through 511 )
4X-RAY DIFFRACTION4chain 'B' and (resid 512 through 524 )
5X-RAY DIFFRACTION5chain 'B' and (resid 525 through 537 )
6X-RAY DIFFRACTION6chain 'B' and (resid 538 through 545 )
7X-RAY DIFFRACTION7chain 'A' and (resid 394 through 421 )
8X-RAY DIFFRACTION8chain 'A' and (resid 422 through 436 )
9X-RAY DIFFRACTION9chain 'A' and (resid 437 through 453 )
10X-RAY DIFFRACTION10chain 'A' and (resid 454 through 462 )
11X-RAY DIFFRACTION11chain 'A' and (resid 463 through 492 )
12X-RAY DIFFRACTION12chain 'A' and (resid 493 through 511 )
13X-RAY DIFFRACTION13chain 'A' and (resid 512 through 524 )
14X-RAY DIFFRACTION14chain 'A' and (resid 525 through 536 )
15X-RAY DIFFRACTION15chain 'A' and (resid 537 through 546 )
16X-RAY DIFFRACTION16chain 'B' and (resid 394 through 408 )
17X-RAY DIFFRACTION17chain 'B' and (resid 409 through 421 )
18X-RAY DIFFRACTION18chain 'B' and (resid 422 through 444 )
19X-RAY DIFFRACTION19chain 'B' and (resid 445 through 462 )

+
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