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- EMDB-51649: CryoEM structure of the native Chlamydomonas reinhardtii Flagella... -

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Basic information

Entry
Database: EMDB / ID: EMD-51649
TitleCryoEM structure of the native Chlamydomonas reinhardtii Flagella Membrane Glycoprotein 1B. Local refinement 1 of 6.
Map dataFlagella membrane glycoprotein 1B. Local refinement 1/6.
Sample
  • Organelle or cellular component: Flagella Membrane Glycoprotein 1B
    • Protein or peptide: Flagella Membrane Glycoprotein 1B
KeywordsMucin / Glycoprotein / Glycocalyx / MEMBRANE PROTEIN
Function / homologymembrane / Uncharacterized protein
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsNievergelt AP / Hoepfner LM / Matrino F / Scholz M / Foster HE / Rodenfels J / von Appen A / Hippler M / Pigino G
Funding support France, European Union, Germany, 4 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)LT000515/2019 France
European Molecular Biology Organization (EMBO)ALTF 891-2018European Union
European Research Council (ERC)819826European Union
German Research Foundation (DFG)HI 739/12-4 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 29, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51649.png

Downloads & links

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Map

FileDownload / File: emd_51649.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFlagella membrane glycoprotein 1B. Local refinement 1/6.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 512 pix.
= 488.96 Å		0.96 Å/pix.
x 512 pix.
= 488.96 Å		0.96 Å/pix.
x 512 pix.
= 488.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.955 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.030438079 - 1.9657367
Average (Standard dev.)0.00021053037 (±0.0071449163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 488.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Flagella membrane glycoprotein 1B. Local refinement 1/6. Halfmap A.

Fileemd_51649_half_map_1.map
AnnotationFlagella membrane glycoprotein 1B. Local refinement 1/6. Halfmap A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Flagella membrane glycoprotein 1B. Local refinement 1/6. Halfmap B.

Fileemd_51649_half_map_2.map
AnnotationFlagella membrane glycoprotein 1B. Local refinement 1/6. Halfmap B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Flagella Membrane Glycoprotein 1B

EntireName: Flagella Membrane Glycoprotein 1B
Components
  • Organelle or cellular component: Flagella Membrane Glycoprotein 1B
    • Protein or peptide: Flagella Membrane Glycoprotein 1B

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Supramolecule #1: Flagella Membrane Glycoprotein 1B

SupramoleculeName: Flagella Membrane Glycoprotein 1B / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Material purified from endogenous Chlamydomonas cilia by lectin affinity chromatography.
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-124 32M fmg1a / Organelle: Cilia / Location in cell: Ciliary membrane
Molecular weightTheoretical: 550 KDa

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Macromolecule #1: Flagella Membrane Glycoprotein 1B

MacromoleculeName: Flagella Membrane Glycoprotein 1B / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-124 32M fmg1a
SequenceString: MAASSPLVRL RRLALPLALV VLCAAAAHGQ TLSSAVLTAS NTIMATLSNV TTSTDCRAAF AYFDSNNATK AASPFANCTV SGTTSVTLI LASGVSYAAG DQLNIKVNQT TLNTTAGVPF VPAAAAAAVQ PVLGAATLTT ASSLVVKLPL SSGNTMPDGY A TNMTICGA ...String:
MAASSPLVRL RRLALPLALV VLCAAAAHGQ TLSSAVLTAS NTIMATLSNV TTSTDCRAAF AYFDSNNATK AASPFANCTV SGTTSVTLI LASGVSYAAG DQLNIKVNQT TLNTTAGVPF VPAAAAAAVQ PVLGAATLTT ASSLVVKLPL SSGNTMPDGY A TNMTICGA AVQLLSAAGA VKASPFSACL LAADTLTLTL TSSGTYAPGD VVNVVAGQST LKNGATSYTK SAAGSVIRPT LT TVSLATT TTILIGASAP VSLPANASAD VCNSIFTVAL KSGTALPTAL SACMAGPAVT AITATFANGT TYSDGLTVTI KAN QTLLRT GDQSASSPLF LPPASALVIA PTVLSASLTS ATSITVQLPV SSTASGTLDA AGCNGAFELR AAGSSASKSS PFSA CALAS NNTALVLTLA SASTYTAGDI FNVKSGQSLL QVGSTAYVPQ AVSVLPTLST AILVAASVVR VGLPVVSSIP APYSA DDCA RSVIIAAANS TAAKAISGCV LSADGKALLV TLGAAYAAGD TVNVRTGQWQ LRAGASVTLG PNYIAASTPV AIVPGF SSA VLTSATQVTV QLPLASALPA TISASECGDA FDLLDASGTT SRVSPWTGCS IGSNNTLVLN MTAGIYVVGD QVTPKSG QT KLTFANTTAY GVLLTPINPI LTAATTAMLT ASSTIVVALP YAANLPASTN NGTVCNAAFD LVSAAGASRT APFSACSI S GGTTLTLTIA STASYTAGDR INVKSGNSAF LGSLSASGPA FVHAGTAIVI TPTVVSTALI SNTNVFVSLS APTSASAFN QSICNGAFDV SGLATPFTNC TLSADGTGIS FLLASAGSVT SGVTTINVKS SQLFLLAAGS GSSDSPAFVP RGSALTISEA KLAGAYLTA ANTIIVKLSV AAAAVDGFSS SCNNVFTLFN SSGTARASPF SACTLSTDGL TVTLTTSSWV STDKLNIRSD Q TLLKVLGA ANGPSYPALS SATEVSPAIT SAHITSPTTI IVPLPVASDL TGSSCSFLVL TAATSNCALS NNGTLLTVTL SG SYTIGDT ININALNSAL RGTSSTGALY QPVSGATAAT IQPTIGAVQV TTSTRLLVTL PAAMSSPVPN PLTADACNAA LDL SGKSSP FAACTASGTT LTLDLASAFV PGDRLNVKST NTALRLGTGA SALFFQPLAT SPANILNPTF VSAKATSTSV VVVS LPAAS TFVKSGSATA GLVKADCDTV LAMSSGSLVG SGNACDLNTT SSSQLIVTLA GTTYAPGQTI NVLTTNTMLL AGSSS GPAY QPRTITINPA YLSSDVVATA PDTVVVTLPV TSGLFAADGS SLGSTLTAAQ CATVLEVKAG TTAKGLASCS LAGTTL TVK LLGNNSDVYT GGDTFNFKDT NALLLAGSAN TAPAYKALAT AAVIVPNLYK AVASAGDTIL ITLPAASTFV VSGSAVL SV SDTVCNTILT FTNSKTVKSG TNCVITGAVL SLTLNSAITD QTTVTINSGG QTTLVSGTGT TGPAYKAGTA APISPAYL T SAAARSATSI VVTLPFTSTV NGATLTKATC DTIVEVLNGG DATKPRTLDS GTPCTLATTL LTVNLAATES FAPGDTVRI KSGNTVLLIG SAGGNAPYVQ ATTATPIALG YVTSSIATKA TEIKVTLPVP ITLIKAGVSV ASLDKTDCDT LLTVASGTLA ATGSCALSG TVLTITTTST YTPGTTTVQF TAVASSASVK ILGGAGTTGT IIAALSAASS VLPGYLTSAV ISGANTFTLT L PYAVTSGG NPTCSDIIEI KAANGAMKTF NGVCSVASAT TVTGTTNEAL LASDTVTLKG AQNALTTTTG SKIYAATAAI NI QPAYLTG AYAIDDKKFV VVLPYASTLA AGTCSSIVSV TDNNNGPAES GCSLALDGTG IYLTVTVSAS LTATAWKVDF KAA QTALTV GSTAWAPMAT GTAKSLNAGA TTWGSSIMTA TAVATNVLEV TLPMSSYMAD ISSGCSPVTF STANTAASCK LIGT TSSPN SILQITLTAG YVAGAVSLAN AAGLIKAGSA SGTAIGAAST VTIKPTFVSA VATGPRTIVV ALPIQSKIIK GAPTC TGGA VTCSSGTATC QSGSPACSAA GTYTCTATDP TVGLTCAAPT VTCPASTTAA CITGGSPGSI ATAGNGPGCA AATTDG GTA ACGAGISAVC YSSSLTTAAR CASGSAFSAA NGNNCDDSAS SIDLDPTCYT SSTMTATAVS DAALCTGWIS GMPTCSS SG KFACVSATGP TCTASTAPTC KSPFTGTANC AITFSCGGTG LVVPTCTGSF TGCSKGTTGD TCDDDIASPA DCSTIFSL T GGTATIAGCS NPGSDFTAPY TTTVTLATAN WVPGTTLSVA ADQAAAAATN YLKPTAAITL LYTTKPSGAV VIYPSISSA TLTGPKSLQV TLPVAASVPS SGLSPADCNN IFQLYATGTT TPKTAAVFSA CYLGADKQTF YLTLAAAAAS TTNANTYAVK DLINIKAGQ SLLKADSATA ANRLAFAPLP DALLIRPAIT SAVATTIASA AVIKMQLPLT SNLGTVNCAT TGIKVRVDDA T DKTQANTG ACSISSDANG AVLTLTLNQA LGASDFTTGK GVSVVVVATS SADATKLQLF GGSDNTGPLY VTGSIPVYDV VT PGQSIVS AKAIASNQVE IKLPAPSTIT TGNTCANFLA FTPTRTISSC VYDAETQLVT ATVDQFAAGD AVNIAGAPNL LKY ATAAAT LTDYAALAAA ATVSPALVSA YTVDSTTIAV VLPATSSFYS GATNSATKVA SLTDVECADV LTVLLAGKTN SAGV SACAT PSNCRTLFSG AACLLGTTSA GDTLLTIKLG ASYAAGDAVD VWDKNAGLNG ATAAAKPLRV GTNVQALYVP RRMPV VIEP RIVSASATGA RTIAVTLPVT SQLIDSTGTV ISAPTQQQCA SLVALPAGKS VASCAISSDF LTLTLTLAAD FAPGDT VNI ASGQTLLRAW KSDVGPGYEL SGPLYTPSAS AVTVTLSFFV SATSTAANTI VVTLPFPVKM YDLAASPAEI LAADGAT PT KDNCDSVIRV IPSGSTIART LVAPGAGVAP CVLSGSGTTI TLTLDTTVSS YATGDRIDVG FGNSANLRGA ATAAAVAN T SPKYTTVATL NAAASAAVVT IGPSIVSAAA ASPTQVKVTL SATGTITTTP ATVDDCNKIV TFTPAKTLAA TSPCSVAGT TLTVNLDKAT PYAGTDAVNI AAANSLAATT NPLKAGSLAF VAKATAVTID PNLYTATAID SLVYEVALPA ASSVGSTALT AAQCGAILS LTGGRTISST VTAPCVLDTT KTLLTVSLGT AYADGDTVTL QSTQATPWLR AASDTGPAYK VGSTLIVKPT I ASAKATTA TTIEVTLPVT SVIWSTSGGA AVSTALTATE CGKILSVKRG SGTVALSASG ACSLSSSGST TLTVTLASDQ VF QAGDKIN ILASNTDSAN TDKYLVATTS SSGQAYIARS SDVVIAPGFI NAAYAVGPNT LSVALPVVSS IATDNDCSTV VTV RASATP TTTRTVSGAC TVASDATGYY LVVTLAAGTP FVSGDEVLIK SGNTALVGSI AYASGAAGAT KPIYANFDDA ILTA PTTVL VTMAAVTTVS FTSKADCDAV FVFSGAGNTT KTTSPIASCA LAPDGLSVTI TLSSADAYVP GDAINVVKDQ TSAKV GGVG GTNLVPYPTA TTISPRPFGA KATLVAPTSV AFSLPAVSSL PAATAAADCN AAVRYTDVAG VDAVNPFTSC ALTPDT KGV VLNTASPIYK AGDVMNIKSG NAAVRWGPQA SGAAYYPAAA DVPVFATVAT ATLVDPSTVV LNLPTVSAIP DNFTVPD CL RAIEFKTAAG VTKNGTVASC MLMPDRLGLQ VKLLSAGNFS AGDTVNIKPE QAELRSSALA TGPSYVPKLA AQVVNPAL F ANANLTSATA ITVRLPFASA LATGADCKAV LALLGAGGVA KNVSSCSLGA DGVTLAVTIP AASFVGGDVL NIVPGQRAL TLADGTTAYV PSKAGVLVTP NIVSATLTNA TIVTVALPTA SVLTSTAAAD CNAAVVIARN GSAVASPLSA CAVSADGLSL TLTAAATYK PMAGDTVDVA VSQTVLRAGS ATGPAYVPRP SPALITVPSP PPSPPPSPAP SPPPSPPLST ANYSARGLAT G PLSCNVLI GDLTVTTTAG NFTTIGMASY AGKDASYKGS CKDAVTGAVY TDDTVASTLP AGLTGLVLSP VTALASVWDL KS VADLANT NKDYLRLFGV PVNASAYGTA VQLLAYDYYV KGFVALETPA VAVLNVEGMV AANLLMYTKF FDGLNTSVAG RDI TAAQAL AAGQYALAAV LEDSIAPINT TDPASILALL NVTYSVLTAN ATSAAGRRLL QTAPAPFTQL QAQATALAAA AAGS NALVA AQQARLITAI NAGTSISAAE LTNIINEASK VIVAQSTVIA TAATGLGSGA ISPASFTSSY TGSALSTLVA QQQLA ATPG SDVTAGPAPS PPSDKKKSNT GLIVGLVVGL VGGAIVITLI VVFIVMRRRK QNVAAAGQAT A

UniProtKB: Uncharacterized protein

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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

Concentration0.2 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
10.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
300.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 297 K / Instrument: LEICA EM GP
DetailsThe is sample lightly clusters but can be separated due to the large size

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.0 K / Max: 77.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 8100 / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 0.75 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 6500000
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 583765
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final 3D classificationNumber classes: 26 / Avg.num./class: 63200 / Software - Name: cryoSPARC (ver. 4.5.1)
FSC plot (resolution estimation)

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