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- PDB-4emz: HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adapti... -

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Basic information

Entry
Database: PDB / ID: 4emz
TitleHIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain)
Components
  • AP-1 complex subunit mu-1AP-1 transcription factor
  • MHC-IMHC class I
  • Protein Nef
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Human immunodeficiency virus 1 / HIV / Nef / MHC-I / antigen presentation / host defense / Adaptor protein complex 1 / Mu1 adaptin subunit / sorting motif recognition / CLASP / membrane trafficking / viral hijacking / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


perturbation by virus of host immune response / negative regulation of CD4 production / AP-1 adaptor complex / endosome to melanosome transport / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization / melanosome assembly / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I ...perturbation by virus of host immune response / negative regulation of CD4 production / AP-1 adaptor complex / endosome to melanosome transport / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization / melanosome assembly / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / Golgi Associated Vesicle Biogenesis / suppression by virus of host autophagy / clathrin adaptor activity / MHC class II antigen presentation / thioesterase binding / CD4 receptor binding / clathrin-coated vesicle / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / host cell Golgi membrane / antigen processing and presentation of exogenous peptide antigen via MHC class I / MHC class I protein binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / detection of bacterium / T cell receptor binding / vesicle-mediated transport / regulation of calcium-mediated signaling / viral life cycle / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / virion component / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / trans-Golgi network / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / SH3 domain binding / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of type II interferon production / Interferon alpha/beta signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / ER-Phagosome pathway / ATPase binding / early endosome membrane / antibacterial humoral response / early endosome / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / signaling receptor binding / innate immune response / endoplasmic reticulum membrane / GTP binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / Mu homology domain, subdomain B / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site ...Nef Regulatory Factor / Nef Regulatory Factor / Mu homology domain, subdomain B / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / AP-1 complex subunit mu-1 / Protein Nef
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsJia, X. / Xiong, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef.
Authors: Jia, X. / Singh, R. / Homann, S. / Yang, H. / Guatelli, J. / Xiong, Y.
History
DepositionApr 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Protein Nef
D: MHC-I
E: MHC-I
B: Protein Nef
A: AP-1 complex subunit mu-1
M: AP-1 complex subunit mu-1


Theoretical massNumber of molelcules
Total (without water)114,3656
Polymers114,3656
Non-polymers00
Water32418
1
C: Protein Nef
D: MHC-I
M: AP-1 complex subunit mu-1


Theoretical massNumber of molelcules
Total (without water)57,1823
Polymers57,1823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-12 kcal/mol
Surface area21590 Å2
MethodPISA
2
E: MHC-I
B: Protein Nef
A: AP-1 complex subunit mu-1


Theoretical massNumber of molelcules
Total (without water)57,1823
Polymers57,1823
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-13 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.324, 112.471, 114.407
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21B
12D
22E
13A
23M

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010C7 - 204
2010B7 - 204
1020D315 - 330
2020E315 - 330
1030A159 - 423
2030M159 - 423

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Protein Nef


Mass: 23586.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: NL-43 / Gene: nef / Production host: Escherichia coli (E. coli) / References: UniProt: Q90VU7
#2: Protein/peptide MHC-I / MHC class I


Mass: 2748.915 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04439*PLUS
#3: Protein AP-1 complex subunit mu-1 / AP-1 transcription factor / AP-mu chain family member mu1A / Adaptor protein complex AP-1 mu-1 subunit / Adaptor-related ...AP-mu chain family member mu1A / Adaptor protein complex AP-1 mu-1 subunit / Adaptor-related protein complex 1 mu-1 subunit / Clathrin assembly protein complex 1 medium chain 1 / Clathrin coat assembly protein AP47 / Clathrin coat-associated protein AP47 / Golgi adaptor HA1/AP1 adaptin mu-1 subunit / Mu-adaptin 1 / Mu1A-adaptin


Mass: 30846.578 Da / Num. of mol.: 2 / Fragment: sorting motif recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1m1, Cltnm / Production host: Escherichia coli (E. coli) / References: UniProt: P35585
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 298 K / Method: microbatch underoil / pH: 6.5
Details: 0.1M HEPES, 3% PEG8000, pH 6.5, Microbatch underoil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorDetector: CCD / Date: Dec 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 26098 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.9-35.71100
3-3.126.21100
3.12-3.276.211000.65
3.27-3.446.211000.423
3.44-3.656.2199.90.25
3.65-3.946.111000.157
3.94-4.336.111000.093
4.33-4.96611000.069
4.96-6.245.9199.90.089
6.24-405.5199.60.07

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.530.1880.1020.53
2Se54.1560.6570.2580.1410.428
3Se600.860.1990.2880.639
4Se25.0910.1690.3370.2940.294
5Se16.7920.210.1750.3820.261
6Se31.1340.2350.1770.4510.269
7Se44.0380.4550.9340.090.271
8Se600.4070.0070.3950.325
9Se10.5420.0140.4650.155
10Se56.5410.3770.9040.0540.235
11Se600.9480.2980.3470.289
12Se600.7840.1720.320.281
13Se24.4870.050.1460.3320.152
Phasing dmFOM : 0.64 / FOM acentric: 0.63 / FOM centric: 0.66 / Reflection: 22301 / Reflection acentric: 19931 / Reflection centric: 2370
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.3-29.8390.930.950.871179852327
5.2-8.30.860.870.7834922946546
4.1-5.20.850.860.7742823798484
3.6-4.10.710.720.6641143752362
3.1-3.60.450.450.4463185857461
2.9-3.10.240.240.2429162726190

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMAC5.6.0116refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.889 / Occupancy max: 1 / Occupancy min: 0.26 / SU B: 43.897 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R: 0.833 / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27795 1317 5.1 %RANDOM
Rwork0.22268 ---
obs0.22543 24623 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 117.856 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2---2.48 Å2-0 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6755 0 0 18 6773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196953
X-RAY DIFFRACTIONr_bond_other_d0.0070.026633
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9559397
X-RAY DIFFRACTIONr_angle_other_deg1.553315257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0785818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86422.738336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.35151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7271562
X-RAY DIFFRACTIONr_chiral_restr0.0930.2981
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217724
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021694
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11C4621X-RAY DIFFRACTIONLOCAL
12B4621X-RAY DIFFRACTIONLOCAL
21D326X-RAY DIFFRACTIONLOCAL
22E326X-RAY DIFFRACTIONLOCAL
31A8386X-RAY DIFFRACTIONLOCAL
32M8386X-RAY DIFFRACTIONLOCAL
LS refinement shellResolution: 2.9→2.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 105 -
Rwork0.374 1765 -
obs--99.1 %
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)
10.5951-1.2740.55463.7854-0.8220.71980.0439-0.11420.0809-0.28020.2016-0.6027-0.0515-0.0993-0.24550.4263-0.09910.10520.355-0.03090.5543-22.1926-31.836111.893
21.5640.56940.3412.62760.61850.2320.23460.03610.135-0.6863-0.0889-0.5743-0.1946-0.0793-0.14570.6074-0.0190.21230.33070.00540.4386-21.1285-39.37252.5189
34.5716-0.7185-2.02840.38751.60387.1820.3864-0.02530.9534-0.1126-0.1633-0.0451-0.0015-0.6934-0.22320.6727-0.181-0.3380.35410.12320.6045-47.8506-13.61681.859
41.4683-1.77930.49643.969-0.02650.4356-0.0669-0.30820.3203-0.174-0.0084-0.36810.0553-0.23230.07530.3562-0.0347-0.01850.3726-0.00190.4998-39.1447-18.887410.9753
50.85261.2943-1.96292.0129-3.08654.76960.19050.38050.31060.04630.59970.5826-0.0102-0.7274-0.79020.40110.1138-0.37240.33480.09541.0226-54.2522-50.41866.2545
61.0052-0.47160.28273.87911.20980.58480.14940.14450.08940.1498-0.1840.08150.09730.06470.03450.4848-0.11970.09550.38540.04980.5012-38.2302-43.339112.6215
71.45751.3816-0.24381.82880.39582.23690.1402-0.13470-0.259-0.10370.3849-0.0377-0.0848-0.03650.5508-0.0031-0.33130.20890.04060.616-42.8819-55.57916.1268
87.2063-3.213-1.8992.2498-1.0715.03830.85330.7094-0.5518-0.4365-0.04610.60520.064-0.7605-0.80720.9060.0318-0.35460.1613-0.00670.7566-39.5824-63.4332-2.6885
91.21850.3624-1.03095.750.98012.4187-0.25570.1884-0.5754-0.91420.0853-0.17690.96170.12520.17040.89980.1217-0.14440.1722-0.10030.3935-33.6572-64.66210.4938
100.11951.27760.465514.76325.35751.9456-0.06760.0492-0.017-0.9337-0.03740.281-0.32250.00060.1050.5422-0.0524-0.06690.4562-0.12540.3093-35.131721.6563.9446
110.40720.0203-1.24650.0043-0.06413.8393-0.0230.1728-0.01530.0186-0.0303-0.0492-0.1287-0.48430.05330.4603-0.0954-0.36210.3772-0.03330.801-46.22297.594913.8053
121.4053-1.76970.7074.118-0.75920.38780.1375-0.0669-0.2391-0.65120.03960.21220.00430.0457-0.17710.50540.0162-0.04950.4831-0.03710.3807-24.00418.082719.0607
134.18120.6622-0.96661.66440.77333.8836-0.1902-0.01110.001-0.3470.03760.3183-0.2918-0.42730.15260.43330.0871-0.10080.35410.02120.4343-41.203627.158317.07
1411.5142-5.7025-0.2474.5023-0.49690.2351-0.2494-0.6491.52970.10.76580.6422-0.0035-0.1455-0.51640.45280.1726-0.13470.2520.21161.3907-41.676136.240323.2209
1523.69891.8891-9.616729.01595.54615.29130.8408-0.2124-0.806-0.4495-0.8217-1.3201-0.4577-0.0463-0.0190.45860.0197-0.03140.5056-0.08480.3572-7.464911.21920.4251
1612.4894-4.6741-2.07333.81551.59830.6846-0.0342-0.00340.2782-0.33510.0283-0.0393-0.1978-0.00440.00590.45030.0248-0.03290.430.05190.2647-21.246927.552324.0279
1710.173710.907110.915716.985810.50911.9992-0.09140.1877-0.02651.86040.1733-0.3213-0.53770.1683-0.08190.7318-0.00250.00210.36360.06930.7011-30.8836-29.260823.1019
185.90450.19370.02621.39850.20420.04370.1496-0.5608-0.6736-0.2541-0.1378-0.065-0.09320.0366-0.01190.4854-0.0886-0.08570.37860.07810.4235-27.071-47.50314.2337
191.47011.2187-0.45145.2847-0.2350.1672-0.3064-0.20810.00040.66140.3401-0.17460.05660.0524-0.03370.52980.0583-0.07610.50750.03210.2619-13.405516.306333.6797
201.831-0.12510.39521.0888-0.94371.8146-0.1533-0.4148-0.17730.53030.28530.0256-0.2369-0.2843-0.1320.53970.14170.04140.4936-0.0270.186-23.166721.553637.9154
210.2101-0.95250.41685.6955-0.63252.12150.0026-0.0163-0.04280.00470.13440.15710.1939-0.1485-0.1370.3116-0.0481-0.11610.39260.07930.4587-17.2454-14.224126.8482
221.3155-0.2304-0.23452.1539-0.66450.2808-0.1042-0.1011-0.08350.08330.08460.0668-0.0343-0.01320.01970.45110.0171-0.04520.46340.03090.3198-17.291715.112128.8891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A159 - 211
2X-RAY DIFFRACTION2A212 - 270
3X-RAY DIFFRACTION3A271 - 288
4X-RAY DIFFRACTION4A289 - 423
5X-RAY DIFFRACTION5B12 - 61
6X-RAY DIFFRACTION6B62 - 82
7X-RAY DIFFRACTION7B83 - 131
8X-RAY DIFFRACTION8B132 - 179
9X-RAY DIFFRACTION9B180 - 203
10X-RAY DIFFRACTION10C8 - 16
11X-RAY DIFFRACTION11C17 - 64
12X-RAY DIFFRACTION12C65 - 81
13X-RAY DIFFRACTION13C82 - 179
14X-RAY DIFFRACTION14C180 - 203
15X-RAY DIFFRACTION15D314 - 319
16X-RAY DIFFRACTION16D320 - 332
17X-RAY DIFFRACTION17E315 - 319
18X-RAY DIFFRACTION18E320 - 331
19X-RAY DIFFRACTION19M159 - 211
20X-RAY DIFFRACTION20M212 - 270
21X-RAY DIFFRACTION21M271 - 381
22X-RAY DIFFRACTION22M382 - 423

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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