[English] 日本語
Yorodumi
- PDB-7a0y: Structure of dimeric sodium proton antiporter NhaA K300R variant,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a0y
TitleStructure of dimeric sodium proton antiporter NhaA K300R variant, at pH 8.2, crystallized with chimeric Fab antibodies
Components
  • (chimeric antibody Fab-F6, ...) x 2
  • Na(+)/H(+) antiporter NhaA
KeywordsMEMBRANE PROTEIN / sodium proton antiporter / transporter / chimeric Fab / antibody
Function / homology
Function and homology information


sodium:proton antiporter activity / regulation of pH / plasma membrane
Similarity search - Function
Na+/H+ antiporter NhaA / Na+/H+ antiporter domain superfamily / Na+/H+ antiporter 1 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / PHOSPHATE ION / Na(+)/H(+) antiporter NhaA
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gallus gallus (chicken)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsFippel, A. / Mir, S.H. / Lentes, C.J. / Wirth, C. / Hunte, C.
Funding support Germany, European Union, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)BIOSS - EXC-294 Germany
German Research Foundation (DFG)CIBSS - EXC-2189 - Project ID 390939984 Germany
German Research Foundation (DFG)CRC - 1381 - Project ID 403222702 Germany
German Research Foundation (DFG)CRC - 746 Germany
European Communitys Seventh Framework ProgrammeEDICT - HEALTH-F4-2007-201924European Union
CitationJournal: To Be Published
Title: Molecular determinants for substrate uptake in electrogenic sodium/proton antiporters
Authors: Fippel, A. / Mir, S.H. / Wirth, C. / Gross, N.M. / Lentes, C.J. / Bialas, E. / Frank, F. / Ulbrich, M.H. / Andrade, S.L.A. / Kulik, A. / Hunte, C.
History
DepositionAug 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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: Na(+)/H(+) antiporter NhaA
B: Na(+)/H(+) antiporter NhaA
C: chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain
D: chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain
E: chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain
F: chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,54019
Polymers185,4926
Non-polymers5,04713
Water2,648147
1
A: Na(+)/H(+) antiporter NhaA
B: Na(+)/H(+) antiporter NhaA
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, assessed by SEC-MALLS (Lentes, C. J. et al. Molecular characterization of the Na+/H+-antiporter NhaA from Salmonella Typhimurium. PloS one 9, e101575, doi:10.1371/journal.pone.0101575 (2014))
  • 93 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)93,00011
Polymers88,0952
Non-polymers4,9059
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-52 kcal/mol
Surface area32940 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19370 Å2
ΔGint-145 kcal/mol
Surface area65970 Å2
MethodPISA
3
C: chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain
D: chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8055
Polymers48,6992
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-54 kcal/mol
Surface area18590 Å2
MethodPISA
4
E: chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain
F: chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7343
Polymers48,6992
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-35 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.036, 91.681, 138.287
Angle α, β, γ (deg.)90.000, 110.076, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Na(+)/H(+) antiporter NhaA / Sodium/proton antiporter NhaA


Mass: 44047.324 Da / Num. of mol.: 2 / Mutation: K300R
Source method: isolated from a genetically manipulated source
Details: K300R variant of NhaA and 5 additional residues at the N-terminus (NLGIL)
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: nhaA, STM0039 / Production host: Escherichia coli (E. coli) / Variant (production host): NM554 / References: UniProt: Q8ZRZ3

-
Antibody , 2 types, 4 molecules CEDF

#2: Antibody chimeric antibody Fab-F6, heavy chain,chimeric antibody Fab-F6, heavy chain


Mass: 26305.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chimeric Fab with avian VH and human CH1 regions,chimeric Fab with avian VH and human CH1 regions
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli) / Variant (production host): JM83
#3: Antibody chimeric antibody Fab-F6, light chain,chimeric antibody Fab-F6, light chain


Mass: 22393.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chimeric Fab with avian VL and human CL regions,chimeric Fab with avian VL and human CL regions
Source: (gene. exp.) Gallus gallus (chicken), (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli (E. coli) / Variant (production host): JM83

-
Non-polymers , 7 types, 160 molecules

#4: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#5: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H77O8P
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 3.9 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 100 mM Tris-HCl pH 8.2, 50 mM BaCl2, 50 mM CaCl2, 30 % PEG400, 0.1 mM 2-aminoperimidine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.45→24.74 Å / Num. obs: 57756 / % possible obs: 94.5 % / Redundancy: 13.7 % / Biso Wilson estimate: 56.88 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.186 / Net I/σ(I): 12.1
Reflection shellResolution: 2.45→2.77 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.854 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2890 / CC1/2: 0.496 / % possible all: 70.2

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX1.13_2998refinement
STARANISOdata scaling
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A0W

7a0w


Resolution: 2.45→24.74 Å / SU ML: 0.2856 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.1039 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2414 1746 3.02 %
Rwork0.2034 56006 -
obs0.2046 57752 59.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.68 Å2
Refinement stepCycle: LAST / Resolution: 2.45→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11897 0 198 147 12242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001612422
X-RAY DIFFRACTIONf_angle_d0.434416905
X-RAY DIFFRACTIONf_chiral_restr0.0391974
X-RAY DIFFRACTIONf_plane_restr0.00362098
X-RAY DIFFRACTIONf_dihedral_angle_d8.86227318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.530.388730.304270X-RAY DIFFRACTION2.83
2.53-2.640.2415270.3093766X-RAY DIFFRACTION8.21
2.64-2.760.3439420.30561526X-RAY DIFFRACTION16.26
2.76-2.90.31931040.29552764X-RAY DIFFRACTION29.6
2.9-3.080.2971710.26825050X-RAY DIFFRACTION53.85
3.08-3.320.282310.25127722X-RAY DIFFRACTION82.15
3.32-3.650.25373070.21499363X-RAY DIFFRACTION99.59
3.65-4.180.24932940.18429435X-RAY DIFFRACTION100
4.18-5.260.20892960.16239447X-RAY DIFFRACTION100
5.26-24.740.22782710.21179663X-RAY DIFFRACTION99.95
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)
11.020234586360.1449629409451.06517851151.58238811923-0.6042148342951.65584065898-0.04885919020190.8738178869150.0384438320353-0.2567697501210.102975361797-0.3758434225750.01601800107830.253616241218-0.05211241213460.5742857529690.06497891851350.09377670785190.809357834388-0.118937798090.30017829575113.12874537552.0419229589131.386062569
22.612742464750.0738050151092-1.440201788393.576802071821.129509254185.470223097760.0005302771673321.13382243829-0.153662512132-1.04343503732-0.105065498226-0.6684605091660.3662805488230.7475456695030.164935914130.6538863805190.1284366040450.1788642284381.00445856186-0.1106867467010.60216610161123.7377062534-1.8111773304328.4736314423
32.01337345917-1.06185136362-0.9078576669651.181695879180.4360882029630.413392963957-0.03660817323260.124862507683-0.774853596806-0.2396984745880.192733539478-0.471435120719-0.0994081865583-0.273961629116-0.1150799098760.787182454858-0.03516789724750.1589807674291.02333883422-0.3096617270930.6200085850770.686069596869-15.053665212829.3226787861
40.696277362177-0.03531862334450.1013709618720.520343949217-0.2020583518241.304207591570.05256223468530.868423290216-0.109240418881-0.525450901097-0.111070369115-0.408317962513-0.04762161601820.207088150511-0.008539330327920.6387905242810.07221200798940.2017432809190.938467074602-0.1189000480030.42316522087314.4417232169-1.538281066225.9756017425
50.719683102727-0.594262646576-0.7448509693363.976704048170.3184046916383.09567031282-0.1076531679271.0628535566-0.224787365741-0.889868171174-0.0458490843254-0.723463949497-0.1545375036990.7595400206740.1302045197510.487079755975-0.01665800201290.1646199520211.0528774381-0.08477185738710.45866525642827.60323757781.8360376002630.6983747138
62.667959369741.23126715152-1.856289319674.52176671737-0.975714036011.29670065943-0.1173218165080.688450563248-0.602240177840.311505288322-0.1948333092170.3173719800160.926436690034-0.2811674192450.386267366790.5963038925130.06681229375930.1138361661530.960145608134-0.1846548608240.47537997274-22.9403365921-6.1474454826626.0477522327
71.28898815319-0.916023512468-1.031196592340.7871374984580.5128481304581.04402283389-0.1182044049711.171836953460.0962879201695-0.544622892219-0.194729411230.304923795908-0.26315407821-0.184845199730.2172090483580.9489142982520.0620088427901-0.09749231724011.596912805510.1302938323550.345139720967-26.578874831711.08861824311.5765170465
82.44750610112-0.190397979452-0.6082230573286.035945914822.267660133633.20355733240.2044051359380.8145522059390.792956087287-0.54293563988-0.269156692346-0.0800131492876-0.5286559106410.2206272086940.07193828573120.8159393819210.00465776431032-0.03065316088541.037582867710.1845392289040.326600349818-8.097575117219.214057504620.8134192056
90.966342617975-0.01540723031490.01880804835051.35297104035-0.02231488879221.90680492495-0.0666253855321.26497725990.307809733515-0.872857100093-0.1287604384660.109510363537-0.204479824137-0.4049892553410.1504946947781.029379837950.0570425709177-0.0541941462191.55357401181-0.03389800057370.254488627709-26.85850359418.0426934838210.7826438367
100.03820090092160.0552963229602-0.389795756230.7668349953831.050971408617.126625986730.2160693390431.082117492490.0298571119321-0.6842988908460.1230760243780.167421140421.44078580224-0.550387161619-0.2940951858350.905121538065-0.0425626912911-0.06141189926261.30800146599-0.1556472414240.343628048044-37.1687985776-0.86120054109711.7910180526
113.5021440867-0.2740384728261.77900491763.0158830633-1.210428234013.850219417640.0986418806667-0.271640160564-0.3067928938620.3547399192710.06651104384210.5099010023080.0251986823064-0.124407949673-0.1296801678880.284123970294-0.03819188675450.0711389524910.0671406017562-0.05858164012310.4813385085428.27737634069-7.8569360448169.2202846849
126.69464331332-3.059184042671.473356259818.42097162306-2.149008935661.35296831390.5554096647380.57266384137-0.431576018036-0.3106402668290.412859371471-0.1181359327520.4072207194050.458942216984-0.5699961388830.231634311963-0.0820285753724-0.00230236204631-0.0413433356997-0.04925192593750.41065396009416.2584898626-6.7369445191860.1733242292
131.195064133180.2381523923260.005245198452152.59789788463-0.1631535432683.02470288561-0.001847562501990.0621584433249-0.3453857898470.165541173770.01197156025370.1671041749330.006256821249640.435718236437-0.04694371470850.1900531927880.03350739275690.0007871509943480.0396242110062-0.06544216387620.26834157001813.5775343172-7.4822881213566.0852448548
146.18203386838-0.724497811605-2.698213542821.404053521481.439439950392.26546151599-0.689803147645-1.35746488393-1.070562012741.414836251550.431582056350.8265894016260.254997428883-0.125496602070.2128323695250.8449718989750.1061716827540.1306515015080.4047391293880.08997577677280.55728073042910.33171671-8.9028286436184.6594183015
157.11669875974-2.95962741441-6.55899458557.585107279886.416591132068.18665633595-0.981223378479-2.8028356573-0.3234084416312.139930058150.3159487958671.57850116076-0.271481449232-0.9188686237550.6505158281121.490899069210.3082876359080.3739273351281.67440544748-0.0992236666130.809991155805-3.008262632920.98102457078299.2128918959
167.54042072751-6.53990976395-5.124829865229.195824385234.795135076056.878289129710.309731851515-0.390320951763-0.712644671360.805370081729-0.693685438081.82380838457-0.2795326408990.006170086328640.4557803743311.18050234415-0.005586023715490.3256174058270.6625526654850.09152465536540.844726770617-0.674763151371-4.6252173547989.4713609321
178.12891088731-3.94800766819-4.73390144276.814187943642.040060923727.48188919446-0.35617478995-0.412316120489-0.5225514781331.24595634636-0.1135493938081.83649076415-0.19918005203-0.4931380011030.4878542519121.125457190350.1744203824970.335865295570.8124471284970.01205966046861.0775582427-5.35369479883-0.51163961055993.5834847769
182.93800207142-0.815284757291-0.6207431103074.197124370941.318183947852.883197508260.0223077755658-0.1040140750370.1514937292540.416347589806-0.1113620782950.343939422493-0.402959442709-0.1550566669910.08297075599740.4026302844090.01637647012560.004378896259330.0703658312125-0.04080332696220.4055239477147.6334862013114.10040019365.4548211037
192.210866186940.2578661847470.7413574076623.09383077038-5.107231890999.02964828337-0.183996156571-1.311488080160.1788562111921.066717602740.2580722794150.281549040527-0.3195866993410.0857201076635-0.05758973074131.752610337270.4660621210620.2567713232231.09615308867-0.1385703632510.6283155003951.7454378564211.093714914899.1483156885
204.661996196211.338484344291.148734568771.5691415079-0.5356691592629.18666346124-0.536250951383-1.244766910070.4753022699291.46268144353-0.1575893091960.389547062441-0.9226049105880.01908741223540.6836253387451.571140343390.3743102757040.1589092826990.986290547724-0.1344394987390.7037280811635.2092371930410.998493559297.3452919821
210.298868422506-0.1107924130180.5885875588570.925640481207-2.52556088517.140897903540.147577550475-0.3762905675290.2474966984810.882376352213-0.0859702303790.101785257312-0.2834853444861.4708974895-0.05826069807212.114690032020.1310117296320.2297329828141.42403857912-0.1580126268630.7072288224751.9464150480519.5817029152103.388897583
226.15179772527-2.06615848596-1.639354369933.522723389650.2713286508623.424814176030.05960241364830.4009966382140.296310538161-0.323099278938-0.106903738835-0.217115361797-0.5747358657970.05844177227780.06544907816070.373930299292-0.0562030747539-0.06805421282050.2207833575770.05640274111670.165756512121-44.551421894518.391464389445.3324135069
232.66057003406-0.517557217191-0.3590973381372.571662327280.3010799209043.739161799340.0122145282626-0.440886729503-0.02007039602810.840621464278-0.0922012709025-0.215311422389-0.01153485352470.0346404337780.04904535051960.426019349292-0.0376596776391-0.1468564462620.162051129095-0.01717069589990.258553043742-59.445257979910.55781904376.2787630151
243.44738903081-0.0325923067166-0.9897696785277.08869006079-2.519860403394.44711313721-0.2477644451170.173499558244-0.854676816197-0.0466063897208-0.1841725984810.04882183293180.5877131340920.2061722020530.3716049933930.2775146940580.02292276726060.1347138602880.239182754352-0.02178687410080.469094268085-39.9061721002-2.0405660488447.6552758297
250.008416650880070.0885260239038-0.1196677229790.765600424666-1.015469140611.34640196980.03249628537650.189381950820.323174402975-0.268474722512-0.25201959272-0.5336501854650.06945121689810.3110551336490.03320365385110.5055280507980.1796263927160.1838331355180.2095036076430.3235856734830.591299999094-46.8818145686-10.675469768865.3689066479
266.00886660289-2.59966890724-0.544100073687.37791586171.706751245122.781055082140.02363637307130.0529340788736-0.1079890946070.081347122084-0.1899227280710.4068445510410.0203785046978-0.08306442321820.1461596927260.300458300245-0.0228173443864-0.01044699530530.08658199196360.0356466505050.262223667206-66.5936347458-3.0466798574471.3948647597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 116 )
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 171 )
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 200 )
4X-RAY DIFFRACTION4chain 'A' and (resid 201 through 313 )
5X-RAY DIFFRACTION5chain 'A' and (resid 314 through 383 )
6X-RAY DIFFRACTION6chain 'B' and (resid 11 through 52 )
7X-RAY DIFFRACTION7chain 'B' and (resid 53 through 173 )
8X-RAY DIFFRACTION8chain 'B' and (resid 174 through 218 )
9X-RAY DIFFRACTION9chain 'B' and (resid 219 through 354 )
10X-RAY DIFFRACTION10chain 'B' and (resid 355 through 383 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 44 )
12X-RAY DIFFRACTION12chain 'C' and (resid 45 through 60 )
13X-RAY DIFFRACTION13chain 'C' and (resid 61 through 112 )
14X-RAY DIFFRACTION14chain 'C' and (resid 113 through 128 )
15X-RAY DIFFRACTION15chain 'C' and (resid 129 through 152 )
16X-RAY DIFFRACTION16chain 'C' and (resid 153 through 166 )
17X-RAY DIFFRACTION17chain 'C' and (resid 167 through 223 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 109 )
19X-RAY DIFFRACTION19chain 'D' and (resid 110 through 146 )
20X-RAY DIFFRACTION20chain 'D' and (resid 147 through 184 )
21X-RAY DIFFRACTION21chain 'D' and (resid 185 through 207 )
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 112 )
23X-RAY DIFFRACTION23chain 'E' and (resid 113 through 223 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 98 )
25X-RAY DIFFRACTION25chain 'F' and (resid 99 through 109 )
26X-RAY DIFFRACTION26chain 'F' and (resid 110 through 209 )

+
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