[English] 日本語
Yorodumi
- PDB-6wrx: Crystal structure of computationally designed protein 2DS25.1 in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wrx
TitleCrystal structure of computationally designed protein 2DS25.1 in complex with the human Transferrin receptor ectodomain
Components
  • Computationally designed protein 2DS25.1
  • Transferrin receptor protein 1
KeywordsDE NOVO PROTEIN/METAL TRANSPORT / Complex / Beta sheet / Receptor / DE NOVO PROTEIN / DE NOVO PROTEIN-METAL TRANSPORT complex
Function / homology
Function and homology information


transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to iron ion / response to copper ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle ...transferrin receptor activity / negative regulation of mitochondrial fusion / transferrin transport / Transferrin endocytosis and recycling / positive regulation of isotype switching / response to iron ion / response to copper ion / response to manganese ion / RND1 GTPase cycle / RND2 GTPase cycle / RHOB GTPase cycle / Golgi Associated Vesicle Biogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / RHOH GTPase cycle / CDC42 GTPase cycle / transport across blood-brain barrier / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of bone resorption / response to retinoic acid / positive regulation of B cell proliferation / clathrin-coated pit / Hsp70 protein binding / positive regulation of T cell proliferation / RAC1 GTPase cycle / cellular response to leukemia inhibitory factor / osteoclast differentiation / response to nutrient / acute-phase response / positive regulation of protein-containing complex assembly / clathrin-coated endocytic vesicle membrane / receptor internalization / HFE-transferrin receptor complex / recycling endosome / positive regulation of protein localization to nucleus / recycling endosome membrane / extracellular vesicle / melanosome / cellular response to xenobiotic stimulus / double-stranded RNA binding / Cargo recognition for clathrin-mediated endocytosis / virus receptor activity / Clathrin-mediated endocytosis / positive regulation of peptidyl-serine phosphorylation / positive regulation of NF-kappaB transcription factor activity / iron ion transport / cytoplasmic vesicle / basolateral plasma membrane / blood microparticle / positive regulation of canonical NF-kappaB signal transduction / intracellular iron ion homeostasis / response to hypoxia / early endosome / endosome membrane / endosome / intracellular signal transduction / positive regulation of protein phosphorylation / external side of plasma membrane / intracellular membrane-bounded organelle / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Transferrin receptor protein 1/2, PA domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
alpha-D-mannopyranose / Transferrin receptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsAbraham, J. / Coscia, A. / Olal, D. / Sahtoe, D.D. / Baker, D. / Clark, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)5R01AG063845-02 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Transferrin receptor targeting by de novo sheet extension.
Authors: Sahtoe, D.D. / Coscia, A. / Mustafaoglu, N. / Miller, L.M. / Olal, D. / Vulovic, I. / Yu, T.Y. / Goreshnik, I. / Lin, Y.R. / Clark, L. / Busch, F. / Stewart, L. / Wysocki, V.H. / Ingber, D.E. ...Authors: Sahtoe, D.D. / Coscia, A. / Mustafaoglu, N. / Miller, L.M. / Olal, D. / Vulovic, I. / Yu, T.Y. / Goreshnik, I. / Lin, Y.R. / Clark, L. / Busch, F. / Stewart, L. / Wysocki, V.H. / Ingber, D.E. / Abraham, J. / Baker, D.
History
DepositionApr 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transferrin receptor protein 1
B: Transferrin receptor protein 1
C: Computationally designed protein 2DS25.1
D: Computationally designed protein 2DS25.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,01812
Polymers164,1904
Non-polymers2,8288
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-36 kcal/mol
Surface area57110 Å2
Unit cell
Length a, b, c (Å)137.425, 137.425, 280.158
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 121 through 759 or resid 803 through 804))A121 - 759
121(chain 'A' and (resid 121 through 759 or resid 803 through 804))A803 - 804
211(chain 'B' and (resid 121 through 668 or (resid 669...B121 - 759
221(chain 'B' and (resid 121 through 668 or (resid 669...B810 - 811
112chain 'C'C1 - 88
212chain 'D'D1 - 88

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Transferrin receptor protein 1 / / Trfr / T9 / p90


Mass: 71807.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFRC / Production host: Escherichia coli (E. coli) / References: UniProt: P02786
#2: Protein Computationally designed protein 2DS25.1


Mass: 10287.801 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)

-
Sugars , 5 types, 6 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 1 types, 2 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.65 Å3/Da / Density % sol: 73.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 12% (w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.067→200 Å / Num. obs: 58129 / % possible obs: 99.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 101.53 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.062 / Net I/σ(I): 9.6
Reflection shellResolution: 3.07→3.25 Å / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 1 / Num. unique obs: 4417 / CC1/2: 0.267 / Rpim(I) all: 0.98 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
XDSJan 26, 2018data processing
pointless1.11.7data reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KAS

3kas


Resolution: 3.07→93.39 Å / SU ML: 0.4141 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6176
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2254 2805 4.87 %
Rwork0.193 54740 -
obs0.1945 57545 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.35 Å2
Refinement stepCycle: LAST / Resolution: 3.07→93.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11573 0 181 0 11754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001812010
X-RAY DIFFRACTIONf_angle_d0.4516277
X-RAY DIFFRACTIONf_chiral_restr0.04251852
X-RAY DIFFRACTIONf_plane_restr0.00262068
X-RAY DIFFRACTIONf_dihedral_angle_d13.95744417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.07-3.120.3693920.34282390X-RAY DIFFRACTION85.26
3.12-3.180.35081110.31872615X-RAY DIFFRACTION96.6
3.18-3.240.35871790.31142672X-RAY DIFFRACTION99.58
3.24-3.30.33211460.32727X-RAY DIFFRACTION99.83
3.3-3.380.35351530.29212708X-RAY DIFFRACTION99.93
3.38-3.450.27591350.27742742X-RAY DIFFRACTION99.97
3.45-3.540.33311340.26252747X-RAY DIFFRACTION99.9
3.54-3.640.2551530.24612718X-RAY DIFFRACTION99.83
3.64-3.740.26091630.22582708X-RAY DIFFRACTION99.93
3.74-3.860.23181210.2132773X-RAY DIFFRACTION100
3.86-40.25071490.20982752X-RAY DIFFRACTION100
4-4.160.25131580.18482745X-RAY DIFFRACTION99.9
4.16-4.350.18451530.17492696X-RAY DIFFRACTION100
4.35-4.580.17551500.15192802X-RAY DIFFRACTION100
4.58-4.870.17211090.1422775X-RAY DIFFRACTION99.86
4.87-5.240.18551450.15772770X-RAY DIFFRACTION99.79
5.25-5.770.21971510.17372774X-RAY DIFFRACTION99.46
5.77-6.610.22141440.19662812X-RAY DIFFRACTION99.97
6.61-8.320.18891460.17222830X-RAY DIFFRACTION99.83
8.33-93.390.19481130.16592984X-RAY DIFFRACTION98.38
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)
13.143813917120.7646666783050.6447268262590.569387790142-0.09205119001360.9608956281350.441506188058-0.661116991296-0.882917722580.279132002308-0.1081661818910.008219143669970.608431937525-0.075894641809-0.3259679400521.073486091760.0320367384937-0.1236554409190.7879473509070.1772139685961.0851061934454.3598812985-0.11661180335410.242736112
27.540781404471.52528324622.553194091712.403489083170.9657772298064.376746582050.0599184878993-0.502562245620.186312855041-0.1916889921560.0468005226838-0.309767188742-0.7188262593830.261949311316-0.103985618740.843778283432-0.04643613799130.01173042230520.765751681061-0.01695692663760.74145240015472.256446689331.115512206714.2337083937
32.566449683470.07786188322820.9931186097792.210941938571.205603849382.415289920550.0424791274285-0.301213888998-0.07847252820370.183332620276-0.0610478084826-0.0672159635086-0.1020337828630.244047459140.01127247348440.818276085260.0140375449638-0.05646694701560.7948293353650.0705863562180.73638429126566.28382971822.738292675711.5356922106
42.209886202-0.7643175714830.244781214742.09903934798-0.03558479303471.677123755970.188284977467-0.596486285714-0.3571090177550.351674278137-0.1383700420910.1695377427790.281846447507-0.181977552113-0.05396501450960.915200669465-0.127528202999-0.03473515128690.8924729042150.1708537745510.79310742202243.88651638547.8980667307112.8768731495
51.823432035740.431348755661-0.07912550563216.77055554648-1.174759264792.229263198670.185925387497-0.5733464720020.1379051865120.3643928312080.04845071134510.917249394219-0.0375167800077-0.48123828123-0.1808709673540.6650160681040.009613466242180.1919813492191.01505103689-0.1051954376520.82974660650327.092269121827.21497227222.66335924647
64.025830112340.555100843704-0.5400281484226.68751686165-1.340973289013.02446964060.0953318300137-0.355959941130.1981701600920.5024301226820.1099521301030.135813818635-0.1269912881140.0842500456379-0.1812613063120.6855581514110.0740319558664-0.005990692776470.806400414325-0.04304754534150.68069873983144.293356698832.283940254-0.294405670106
70.5431793936440.6825677598360.8080740018723.429339125651.188412934081.85077371295-0.1498788555020.215514515187-0.0611930089497-0.2282479935070.2507785768090.1010417296810.0434854135099-0.478283714323-0.09384222009110.7160609007660.1911851601860.1046750651790.874102018969-0.04886990515780.62840161918330.529868454232.2533717952-6.75781595866
81.275124344381.179445952110.06191867956667.134250048-0.2622352394621.91020172137-0.3728138513180.4495250511970.0786394692629-0.7950787122030.691408673750.9128059464250.0419867691937-0.461517485677-0.1877782935430.7147378297370.140815483108-0.2248893387541.03803320008-0.1183999000271.1355029737614.433152617324.3088797305-36.6963570518
91.285583308290.599893105490.1554729793251.15383418603-0.7998498745881.211713434530.1274035697740.04199400960670.145198760803-0.0855607997406-0.02183720387910.49605664468-0.188169531638-0.482927652098-0.2125987344590.7473840671670.3351542177710.03503427429340.884022967173-0.0835007038510.93397992928923.911094710841.1221820122-27.544987443
102.522964516071.79403216089-0.4720515858223.17542980531-1.054668161162.39881474535-0.04068574299990.1215095428950.0704087228087-0.2461503908570.11559171285-0.2713461958570.339540477980.1547298945520.1269438670450.8217332568390.2356481225010.05105828457240.7619037511120.03048545679360.70925284206250.818942073644.5516199016-40.5448209284
111.778105627990.636271206685-0.8999072846642.52625956209-0.8193385156241.92094143307-0.02670708367990.1908625581540.00992828054427-0.390350228797-0.205831231379-0.0896251528699-0.1760777652710.02432908959740.05440407637430.7401705314640.2708204600420.03358807079290.784992826698-0.0351026349830.77720157399641.876773956142.1056791616-36.4830874687
122.477502726431.12904915885-0.6739979278742.28693728371-0.2379893836630.5285010953720.1224244260830.18854225973-0.025965551812-0.161530587226-0.166305866070.271977450531-0.0125702412081-0.207734561165-0.03985750272390.7048211585230.18168616389-0.1360887782180.801479030216-0.00308143816610.70652392349828.779236600133.744982985-32.8893948131
131.69945480121-0.259479434036-0.1964283059392.666858117070.09803179543171.545657502690.1062687335370.113491386841-0.211590248114-0.449552095118-0.04202836862190.3927253531110.11329072578-0.0889883646655-0.04386648973030.7692734826070.112186934715-0.09762545796910.746093656797-0.06758281092710.90803240902329.63828602219.8479427427-32.4461356237
142.00115747260.879132624052-0.4447018491092.66847221134-0.4318419335142.23452001370.01566204440880.3054559074390.0132198072286-0.57857384905-0.2452459998250.1666470554180.172020072690.001494658966860.08012164892870.7499597901080.234360321552-0.1213181183330.860677254015-0.1486862137790.80046485298924.067902161823.8699823114-41.1641906276
158.356169032290.921394315588-1.284594863712.45234583577-0.214612683212.23350002621-0.07172765250730.338116433313-1.19913508853-0.271524798516-0.00941621904569-0.1693119152790.737411210130.01357804477550.1210156208560.9417770880870.166526193467-0.03600184806060.61850337664-0.1023192873340.77451746433144.4863551234.09670575918-23.7867267086
166.314473377081.70601095175-0.9691850748984.131784331210.6243777389822.711743496490.176688669940.281959569834-0.137881821783-0.478960660018-0.231949067040.254158162783-0.1467519545020.1470670348330.02136069272270.6935154642390.237416261477-0.01690070338820.6938102244150.01596432464410.65914914892651.450631830220.6726560138-24.0180336674
174.478915110094.27899792623-3.546571179345.14038391321-1.99615921785.289337603240.666425525210.0955110333798-1.078096063350.660135064624-0.541591423417-0.4983580279890.484580256178-0.2014510495910.2346413346940.8918235092740.143683207675-0.1981737507520.6173600841620.008939176963470.77694790857151.56673094767.95387250738-16.0626494994
182.53330495267-3.213253648543.26731419375.47604858214-1.644196893179.66734459941-0.263090674208-0.9802559865211.972264119470.630327916981-0.1383107250470.34128347947-0.938433743226-1.13786844680.5861849985651.211530112510.1450003200650.1687757439641.01970551642-0.01169880223541.1970661756743.496035572978.1191440869-40.9242069813
192.887270987893.57867109963.457230567784.42224636364.26826471274.15354434268-0.134238835883-1.556101194850.1642117635531.79983999859-0.0638185240639-0.02859890748240.0180140996910.02318576882520.1626984349591.081585451740.2265563085470.009506410898591.06016124177-0.04436717763810.90067746052549.203445353668.9834058313-39.6317883637
206.57881666144-6.1746365468-0.8715381135517.929602537525.181152628029.470444154380.1841667017210.3604352441111.4135649944-0.319058088474-0.0751138971327-0.355465316294-0.585838226619-0.526614697188-0.08036041137120.8977408352120.104684515445-0.1316643611820.602813792282-0.03921285637450.74179362414449.27435069869.9418828238-48.7167457592
218.621485238263.454863874133.071643117748.128754435620.7063827050833.17393308544-0.3027503656430.8096755037360.58624282392-0.6687777843250.1710359013670.09931361097650.03120930779210.3408193353390.1524377620290.8417237613270.1922273650990.07542099072970.7411211577940.09021955144460.66771313104347.575928702968.7704266742-56.7847524485
223.96552098497-2.037893256412.978447914016.108000915110.590815783363.08433430778-0.2504711317880.702658631308-0.151360575533-0.9234953773510.272133933821-1.03238397489-0.08995865594810.8369894086890.222900899561.10352649462-0.151639336651-0.0165215375552.17293176555-0.2346561953041.30888686573101.22336676618.624615757910.4102864061
235.12037294063-0.7130773790782.187366587027.784824578731.504068004628.64721658835-0.2299339200061.336943602050.182602527352-0.419701516670.102148288175-0.821346252673-0.1423866746891.576930755130.2340635845750.992953579231-0.2240496133550.05777488103741.67386832135-0.09405497199950.91175953638893.910105954526.207692844913.5073802991
244.81562479023-4.261719072751.912397886317.058510864742.80783566797.175539589990.3048029466081.539746647960.2169844013530.2767623861550.763327550309-1.566954135880.1407219204372.04886495781-0.8481675846350.743481268409-0.1244291013930.02821087439221.44131684680.03175333705081.3605229286298.822658562225.505832800925.9918316564
256.06918847808-3.151427794910.3876604839163.45021751793-2.431405738572.881655827830.230987635621-0.523750602936-0.03556488721660.2624083470590.3466248401031.19656353886-0.00850343394229-1.03021221748-0.5660824321791.08429274244-0.1145118816790.0847876784691.1784978995-0.02470768047830.95356769492788.228155945127.973491701228.4575225959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 121 through 204 )
2X-RAY DIFFRACTION2chain 'A' and (resid 205 through 253 )
3X-RAY DIFFRACTION3chain 'A' and (resid 254 through 393 )
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 610 )
5X-RAY DIFFRACTION5chain 'A' and (resid 611 through 679 )
6X-RAY DIFFRACTION6chain 'A' and (resid 680 through 728 )
7X-RAY DIFFRACTION7chain 'A' and (resid 729 through 759 )
8X-RAY DIFFRACTION8chain 'B' and (resid 121 through 159 )
9X-RAY DIFFRACTION9chain 'B' and (resid 160 through 204 )
10X-RAY DIFFRACTION10chain 'B' and (resid 205 through 282 )
11X-RAY DIFFRACTION11chain 'B' and (resid 283 through 357 )
12X-RAY DIFFRACTION12chain 'B' and (resid 358 through 439 )
13X-RAY DIFFRACTION13chain 'B' and (resid 440 through 558 )
14X-RAY DIFFRACTION14chain 'B' and (resid 559 through 610 )
15X-RAY DIFFRACTION15chain 'B' and (resid 611 through 679 )
16X-RAY DIFFRACTION16chain 'B' and (resid 680 through 727 )
17X-RAY DIFFRACTION17chain 'B' and (resid 728 through 760 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 15 )
19X-RAY DIFFRACTION19chain 'C' and (resid 16 through 29 )
20X-RAY DIFFRACTION20chain 'C' and (resid 30 through 40 )
21X-RAY DIFFRACTION21chain 'C' and (resid 41 through 88 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 15 )
23X-RAY DIFFRACTION23chain 'D' and (resid 16 through 40 )
24X-RAY DIFFRACTION24chain 'D' and (resid 41 through 73 )
25X-RAY DIFFRACTION25chain 'D' and (resid 74 through 88 )

+
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