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- EMDB-20217: Structure of SIVsmm Nef and SMM tetherin bound to the clathrin ad... -

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Entry
Database: EMDB / ID: EMD-20217
TitleStructure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex
Map data
Sample
  • Complex: Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex
    • Protein or peptide: AP-2 complex subunit alpha
    • Protein or peptide: AP-2 complex subunit beta
    • Protein or peptide: Adaptor protein complex AP-2, mu1
    • Protein or peptide: Tetherin,Protein Nef
    • Protein or peptide: AP-2 complex subunit sigma
KeywordsAP / HIV / Nef / trafficking / Protein transport / viral restriction factor
Function / homology
Function and homology information


AP-type membrane coat adaptor complex / Formation of annular gap junctions / Gap junction degradation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / clathrin coat / postsynaptic endocytic zone / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance ...AP-type membrane coat adaptor complex / Formation of annular gap junctions / Gap junction degradation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / clathrin coat / postsynaptic endocytic zone / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / Trafficking of GluR2-containing AMPA receptors / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / WNT5A-dependent internalization of FZD4 / VLDLR internalisation and degradation / extrinsic component of presynaptic endocytic zone membrane / clathrin adaptor complex / cardiac septum development / metalloendopeptidase inhibitor activity / Recycling pathway of L1 / MHC class II antigen presentation / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / Recycling pathway of L1 / Clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / membrane coat / vesicle budding from membrane / positive regulation of protein localization to membrane / clathrin-dependent endocytosis / MHC class II antigen presentation / signal sequence binding / coronary vasculature development / aorta development / ventricular septum development / Neutrophil degranulation / clathrin binding / low-density lipoprotein particle receptor binding / Trafficking of GluR2-containing AMPA receptors / positive regulation of endocytosis / positive regulation of receptor internalization / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / vesicle-mediated transport / protein serine/threonine kinase binding / phosphatidylinositol binding / secretory granule / kidney development / intracellular protein transport / cytoplasmic side of plasma membrane / kinase binding / disordered domain specific binding / synaptic vesicle / heart development / protein-containing complex assembly / cytoplasmic vesicle / defense response to virus / transmembrane transporter binding / postsynapse / protein domain specific binding / innate immune response / intracellular membrane-bounded organelle / synapse / lipid binding / protein-containing complex binding / protein kinase binding / GTP binding / host cell plasma membrane / glutamatergic synapse / cell surface / Golgi apparatus / mitochondrion / membrane / plasma membrane
Similarity search - Function
Bone marrow stromal antigen 2 / Bone marrow stromal antigen 2 / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain ...Bone marrow stromal antigen 2 / Bone marrow stromal antigen 2 / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / HIV negative factor Nef / AP-1/2/4 complex subunit beta / Adaptor protein complex, sigma subunit / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / : / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / Adaptor complexes medium subunit family / AP-2 complex subunit mu, C-terminal superfamily / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Longin-like domain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Tetherin variant Sm2 / AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit beta / AP-2 complex subunit mu / Protein Nef / AP-2 complex subunit mu / AP-2 complex subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse) / Simian immunodeficiency virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBuffalo CZ / Ren X
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 GM125209 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI120691 United States
CitationJournal: Cell Host Microbe / Year: 2019
Title: Structural Basis for Tetherin Antagonism as a Barrier to Zoonotic Lentiviral Transmission.
Authors: Cosmo Z Buffalo / Christina M Stürzel / Elena Heusinger / Dorota Kmiec / Frank Kirchhoff / James H Hurley / Xuefeng Ren /
Abstract: Tetherin is a host defense factor that physically prevents virion release from the plasma membrane. The Nef accessory protein of simian immunodeficiency virus (SIV) engages the clathrin adaptor AP-2 ...Tetherin is a host defense factor that physically prevents virion release from the plasma membrane. The Nef accessory protein of simian immunodeficiency virus (SIV) engages the clathrin adaptor AP-2 to downregulate tetherin via its DIWK motif. As human tetherin lacks DIWK, antagonism of tetherin by Nef is a barrier to simian-human transmission of non-human primate lentiviruses. To determine the molecular basis for tetherin counteraction, we reconstituted the AP-2 complex with a simian tetherin and SIV Nef and determined its structure by cryoelectron microscopy (cryo-EM). Nef refolds the first α-helix of the β2 subunit of AP-2 to a β hairpin, creating a binding site for the DIWK sequence. The tetherin binding site in Nef is distinct from those of most other Nef substrates, including MHC class I, CD3, and CD4 but overlaps with the site for the restriction factor SERINC5. This structure explains the dependence of SIVs on tetherin DIWK and consequent barrier to human transmission.
History
DepositionMay 10, 2019-
Header (metadata) releaseAug 21, 2019-
Map releaseSep 25, 2019-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.485
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.485
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6owt
  • Surface level: 0.485
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20217.png

Downloads & links

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Map

FileDownload / File: emd_20217.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 256 pix.
= 294.144 Å		1.15 Å/pix.
x 256 pix.
= 294.144 Å		1.15 Å/pix.
x 256 pix.
= 294.144 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.149 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.485 / Movie #1: 0.485
Minimum - Maximum-2.185999 - 3.475225
Average (Standard dev.)0.0033728944 (±0.06059342)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 294.144 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1491.1491.149
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z294.144294.144294.144
α/β/γ90.00090.00090.000
start NX/NY/NZ1548552
NX/NY/NZ198170217
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.1863.4750.003

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Supplemental data

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Sample components

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Entire : Structure of SIVsmm Nef and SMM tetherin bound to the clathrin ad...

EntireName: Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex
Components
  • Complex: Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex
    • Protein or peptide: AP-2 complex subunit alpha
    • Protein or peptide: AP-2 complex subunit beta
    • Protein or peptide: Adaptor protein complex AP-2, mu1
    • Protein or peptide: Tetherin,Protein Nef
    • Protein or peptide: AP-2 complex subunit sigma

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Supramolecule #1: Structure of SIVsmm Nef and SMM tetherin bound to the clathrin ad...

SupramoleculeName: Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 203.6 KDa

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Macromolecule #1: AP-2 complex subunit alpha

MacromoleculeName: AP-2 complex subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 104.286391 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPAVSKGEGM RGLAVFISDI RNCKSKEAEI KRINKELANI RSKFKGDKAL DGYSKKKYVC KLLFIFLLGH DIDFGHMEAV NLLSSNRYT EKQIGYLFIS VLVNSNSELI RLINNAIKND LASRNPTFMG LALHCIANVG SREMAEAFAG EIPKILVAGD T MDSVKQSA ...String:
MPAVSKGEGM RGLAVFISDI RNCKSKEAEI KRINKELANI RSKFKGDKAL DGYSKKKYVC KLLFIFLLGH DIDFGHMEAV NLLSSNRYT EKQIGYLFIS VLVNSNSELI RLINNAIKND LASRNPTFMG LALHCIANVG SREMAEAFAG EIPKILVAGD T MDSVKQSA ALCLLRLYRT SPDLVPMGDW TSRVVHLLND QHLGVVTAAT SLITTLAQKN PEEFKTSVSL AVSRLSRIVT SA STDLQDY TYYFVPAPWL SVKLLRLLQC YPPPEDPAVR GRLTECLETI LNKAQEPPKS KKVQHSNAKN AVLFEAISLI IHH DSEPNL LVRACNQLGQ FLQHRETNLR YLALESMCTL ASSEFSHEAV KTHIETVINA LKTERDVSVR QRAVDLLYAM CDRS NAQQI VAEMLSYLET ADYSIREEIV LKVAILAEKY AVDYTWYVDT ILNLIRIAGD YVSEEVWYRV IQIVINRDDV QGYAA KTVF EALQAPACHE NLVKVGGYIL GEFGNLIAGD PRSSPLIQFN LLHSKFHLCS VPTRALLLST YIKFVNLFPE VKATIQ DVL RSDSQLKNAD VELQQRAVEY LRLSTVASTD ILATVLEEMP PFPERESSIL AKLKKKKGPS TVTDLEETKR ERSIDVN GG PEPVPASTSA ASTPSPSADL LGLGAVPPAP TGPPPTSGGG LLVDVFSDSA SAVAPLAPGS EDNFARFVCK NNGVLFEN Q LLQIGLKSEF RQNLGRMFIF YGNKTSTQFL NFTPTLICAD DLQTNLNLQT KPVDPTVDGG AQVQQVVNIE CISDFTEAP VLNIQFRYGG TFQNVSVKLP ITLNKFFQPT EMASQDFFQR WKQLSNPQQE VQNIFKAKHP MDTEITKAKI IGFGSALLEE VDPNPANFV GAGIIHTKTT QIGCLLRLEP NLQAQMYRLT LRTSKDTVSQ RLCELLSEQF

UniProtKB: AP-2 complex subunit alpha

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Macromolecule #2: AP-2 complex subunit beta

MacromoleculeName: AP-2 complex subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 66.953195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDSKYFTTN KKGEIFELKA ELNNEKKEKR KEAVKKVIAA MTVGKDVSSL FPDVVNCMQT DNLELKKLVY LYLMNYAKSQ PDMAIMAVN SFVKDCEDPN PLIRALAVRT MGCIRVDKIT EYLCEPLRKC LKDEDPYVRK TAAVCVAKLH DINAQMVEDQ G FLDSLRDL ...String:
MTDSKYFTTN KKGEIFELKA ELNNEKKEKR KEAVKKVIAA MTVGKDVSSL FPDVVNCMQT DNLELKKLVY LYLMNYAKSQ PDMAIMAVN SFVKDCEDPN PLIRALAVRT MGCIRVDKIT EYLCEPLRKC LKDEDPYVRK TAAVCVAKLH DINAQMVEDQ G FLDSLRDL IADSNPMVVA NAVAALSEIS ESHPNSNLLD LNPQNINKLL TALNECTEWG QIFILDCLSN YNPKDDREAQ SI CERVTPR LSHANSAVVL SAVKVLMKFL ELLPKDSDYY NMLLKKLAPP LVTLLSGEPE VQYVALRNIN LIVQKRPEIL KQE IKVFFV KYNDPIYVKL EKLDIMIRLA SQANIAQVLA ELKEYATEVD VDFVRKAVRA IGRCAIKVEQ SAERCVSTLL DLIQ TKVNY VVQEAIVVIR DIFRKYPNKY ESIIATLCEN LDSLDEPDAR AAMIWIVGEY AERIDNADEL LESFLEGFHD ESTQV QLTL LTAIVKLFLK KPSETQELVQ QVLSLATQDS DNPDLRDRGY IYWRLLSTDP VTAKEVVLSE KPLISEETDL IEPTLL DEL ICHIGSLASV YHKPPNAFVE GSHGIHRK

UniProtKB: AP-2 complex subunit beta

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Macromolecule #3: Adaptor protein complex AP-2, mu1

MacromoleculeName: Adaptor protein complex AP-2, mu1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 16.161563 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIGGLFIYNH KGEVLISRVY RDDIGRNAVD AFRVNVIHAR QQVRSPVTNI ARTSFFHVKR SNIWLAAVTK QNVNAAMVFE FLYKMCDVM AAYFGKISEE NIKNNFVLIY ELLDEILDFG YPQNSETGAL KTFITQQGIK SQ

UniProtKB: AP-2 complex subunit mu

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Macromolecule #4: Tetherin,Protein Nef

MacromoleculeName: Tetherin,Protein Nef / type: protein_or_peptide / ID: 4
Details: protein chimera of the cytoplasmic tail of sooty mangabey (smm) linked to the N-terminus of SIV smm tetherin
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Simian immunodeficiency virus
Molecular weightTheoretical: 31.772352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ILYDYSRMPM GDIWKEDGDK RSKGSDEASE GSGMGGVTSK KQSKRRQGLR ERLLQARGET DGYSRSRGEL GKGWNLPSAE GQGYSEEQF MNTPWRNPAR EGEKLKYRQQ NMDDVDDDDD ELVGVAVHPK VPLRAMSYKL AIDMSHFIKE KGGLEGIYYS D RRHRILDI ...String:
ILYDYSRMPM GDIWKEDGDK RSKGSDEASE GSGMGGVTSK KQSKRRQGLR ERLLQARGET DGYSRSRGEL GKGWNLPSAE GQGYSEEQF MNTPWRNPAR EGEKLKYRQQ NMDDVDDDDD ELVGVAVHPK VPLRAMSYKL AIDMSHFIKE KGGLEGIYYS D RRHRILDI YLEKEEGIIP DWQNYTSGPG VRYPLFFGWL WKLVPVNVSD EAQEDETHCL VHPAQTSQWD DPWGEVLAWK FD PKLAYTY EAFIRYPEEF GNDSGLSKEE VKRRLTAR

UniProtKB: Tetherin variant Sm2, Protein Nef

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Macromolecule #5: AP-2 complex subunit sigma

MacromoleculeName: AP-2 complex subunit sigma / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 17.011662 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIRFILIQNR AGKTRLAKWY MQFDDDEKQK LIEEVHAVVT VRDAKHTNFV EFRNFKIIYR RYAGLYFCIC VDVNDNNLAY LEAIHNFVE VLNEYFHCVS ELDLVFNFYK VYTVVDEMFL AGEIRETSQT KVLKQLLMLQ SLE

UniProtKB: AP-2 complex subunit sigma

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 8
GridModel: C-flat-2/1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa / Details: 25mA
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.16 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159406
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4nee

source_name: PDB, initial_model_type: experimental model

2xa7

source_name: PDB, initial_model_type: experimental model
Output model

PDB-6owt:
Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex

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