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- EMDB-46606: Cryo-EM structure of BG505 DS-SOSIP.664 with 2 CH103 KN Fabs bound -

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Basic information

Entry
Database: EMDB / ID: EMD-46606
TitleCryo-EM structure of BG505 DS-SOSIP.664 with 2 CH103 KN Fabs bound
Map data
Sample
  • Complex: BG505 HIV-1 Env with 2 CH103 K75 N76 Fabs bound
    • Protein or peptide: Surface protein gp120
    • Protein or peptide: Transmembrane protein gp41
    • Protein or peptide: CH103 K75 N76 Fab heavy chain
    • Protein or peptide: CH103 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsTrimer / Env / BG505 / CH103 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsParsons RJ / Acharya P
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145687 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI170752 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U01 AI169587 United States
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
DepositionAug 16, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46606.png

Downloads & links

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Map

FileDownload / File: emd_46606.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.634578 - 0.97218907
Average (Standard dev.)-0.00017660874 (±0.026153842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46606_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46606_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BG505 HIV-1 Env with 2 CH103 K75 N76 Fabs bound

EntireName: BG505 HIV-1 Env with 2 CH103 K75 N76 Fabs bound
Components
  • Complex: BG505 HIV-1 Env with 2 CH103 K75 N76 Fabs bound
    • Protein or peptide: Surface protein gp120
    • Protein or peptide: Transmembrane protein gp41
    • Protein or peptide: CH103 K75 N76 Fab heavy chain
    • Protein or peptide: CH103 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BG505 HIV-1 Env with 2 CH103 K75 N76 Fabs bound

SupramoleculeName: BG505 HIV-1 Env with 2 CH103 K75 N76 Fabs bound / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4, #3
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Surface protein gp120

MacromoleculeName: Surface protein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 55.359906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAAENLWV TVYYGVPVWK DAETTLFCAS DAKAYETEKH NVWATHACVP TDPNPQEIHL ENVTEEFNM WKNNMVEQMH TDIISLWDQS LKPCVKLTPL CVTLQCTNVT NNITDDMRGE LKNCSFNMTT ELRDKKQKVY S LFYRLDVV ...String:
MPMGSLQPLA TLYLLGMLVA SVLAAENLWV TVYYGVPVWK DAETTLFCAS DAKAYETEKH NVWATHACVP TDPNPQEIHL ENVTEEFNM WKNNMVEQMH TDIISLWDQS LKPCVKLTPL CVTLQCTNVT NNITDDMRGE LKNCSFNMTT ELRDKKQKVY S LFYRLDVV QINENQGNRS NNSNKEYRLI NCNTSACTQA CPKVSFEPIP IHYCAPAGFA ILKCKDKKFN GTGPCPSVST VQ CTHGIKP VVSTQLLLNG SLAEEEVMIR SENITNNAKN ILVQFNTPVQ INCTRPNNNT RKSIRIGPGQ AFYATGDIIG DIR QAHCNV SKATWNETLG KVVKQLRKHF GNNTIIRFAN SSGGDLEVTT HSFNCGGEFF YCNTSGLFNS TWISNTSVQG SNST GSNDS ITLPCRIKQI INMWQRIGQC MYAPPIQGVI RCVSNITGLI LTRDGGSTNS TTETFRPGGG DMRDNWRSEL YKYKV VKIE PLGVAPTRCK RR

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Macromolecule #2: Transmembrane protein gp41

MacromoleculeName: Transmembrane protein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 18.344963 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VVGRRRRRRA VGIGAVFLGF LGAAGSTMGA ASMTLTVQAR NLLSGIVQQQ SNLLRAPEAQ QHLLKLTVWG IKQLQARVLA VERYLRDQQ LLGIWGCSGK LICCTNVPWN SSWSNRNLSE IWDNMTWLQW DKEISNYTQI IYGLLEESQN QQEKNEQDLL A LD

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Macromolecule #3: CH103 Fab light chain

MacromoleculeName: CH103 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.530268 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGSWAS YELTQPPSVS VSPGQTATIT CSGASTNVCW YQVKPGQSPE VVIFENYKRP SGIPDRFSGS KSGSTATLT IRGTQAIDEA DYYCQVWDSF STFVFGSGTQ VTVLGQPKAN PTVTLFPPSS EELQANKATL VCLISDFYPG A VTVAWKAD ...String:
MGWSCIILFL VATATGSWAS YELTQPPSVS VSPGQTATIT CSGASTNVCW YQVKPGQSPE VVIFENYKRP SGIPDRFSGS KSGSTATLT IRGTQAIDEA DYYCQVWDSF STFVFGSGTQ VTVLGQPKAN PTVTLFPPSS EELQANKATL VCLISDFYPG A VTVAWKAD SSPVKAGVET TTPSKQSNNK YAASSYLSLT PEQWKSHRSY SCQVTHEGST VEKTVAPTEC S

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Macromolecule #4: CH103 K75 N76 Fab heavy chain

MacromoleculeName: CH103 K75 N76 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.885307 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ VQLQESGPGV VKSSETLSLT CTVSGGSMGG TYWSWLRLSP GKGLEWIGYI FHTGETNYSP SLKGRVSIS VDTSKNQFSL RLRSVTAADT AVYFCASLPR GQLVNAYFRN WGRGSLVSVT AASTKGPSVF PLAPSSKSTS G GTAALGCL ...String:
MGWSCIILFL VATATGVHSQ VQLQESGPGV VKSSETLSLT CTVSGGSMGG TYWSWLRLSP GKGLEWIGYI FHTGETNYSP SLKGRVSIS VDTSKNQFSL RLRSVTAADT AVYFCASLPR GQLVNAYFRN WGRGSLVSVT AASTKGPSVF PLAPSSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EP KSCDK

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 30 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295.15 K / Instrument: LEICA EM GP / Details: Leica EM GP2.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe data were processed in cryoSPARCv4.01. Movies were aligned using Patch Motion Correction and the non-dose weighted aligned micrographs were used for the CTF correction with PatchCTF Estimation.
Particle selectionNumber selected: 997941
CTF correctionDetails: CryoSPARCv4.01 Patch motion correction and CTF estimation jobs
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 73518
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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