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- EMDB-25814: Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH... -

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Basic information

Entry
Database: EMDB / ID: EMD-25814
TitleCryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.SOSIP.664 with high-mannose glycans
Map dataCryo-EM map of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.SOSIP.664 with high-mannose glycans
Sample
  • Complex: Trimeric HIV-1 Env in complex with CH235.12
    • Protein or peptide: Glycoprotein 41
    • Protein or peptide: CH235.12 Fab Heavy Chain
    • Protein or peptide: CH235.12 Fab Light Chain
  • Protein or peptide: Envelope glycoprotein gp160
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose
KeywordsHIV-1 / VIRAL PROTEIN-IMMUNE SYSTEM complex / CH235.12 / IMMUNE SYSTEM / complex glycans / CH505TF / SOSIP / VIRAL PROTEIN
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsManne K / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI45687 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.G458Y.SOSIP.664
Authors: Manne K
History
DepositionDec 27, 2021-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateAug 2, 2023-
Current statusAug 2, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25814.png

Downloads & links

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Map

FileDownload / File: emd_25814.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.SOSIP.664 with high-mannose glycans
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-0.5866629 - 3.0368962
Average (Standard dev.)0.0036243866 (±0.12682146)
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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Sample components

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Entire : Trimeric HIV-1 Env in complex with CH235.12

EntireName: Trimeric HIV-1 Env in complex with CH235.12
Components
  • Complex: Trimeric HIV-1 Env in complex with CH235.12
    • Protein or peptide: Glycoprotein 41
    • Protein or peptide: CH235.12 Fab Heavy Chain
    • Protein or peptide: CH235.12 Fab Light Chain
  • Protein or peptide: Envelope glycoprotein gp160
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: Trimeric HIV-1 Env in complex with CH235.12

SupramoleculeName: Trimeric HIV-1 Env in complex with CH235.12 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.456352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAAENLWV TVYYGVPVWK EAKTTLFCAS DAKAYEKKVH NVWATHACVP TDPNPQEMVL KNVTENFNM WKNDMVDQMH EDVISLWDQS LKPCVKLTPL CVTLNCTNAT ASNSSIIEGM KNCSFNITTE LRDKREKKNA L FYKLDIVQ ...String:
MPMGSLQPLA TLYLLGMLVA SVLAAENLWV TVYYGVPVWK EAKTTLFCAS DAKAYEKKVH NVWATHACVP TDPNPQEMVL KNVTENFNM WKNDMVDQMH EDVISLWDQS LKPCVKLTPL CVTLNCTNAT ASNSSIIEGM KNCSFNITTE LRDKREKKNA L FYKLDIVQ LDGNSSQYRL INCNTSVITQ ACPKVSFDPI PIHYCAPAGY AILKCNNKTF TGTGPCNNVS TVQCTHGIKP VV STQLLLN GSLAEGEIII RSENITKNVK TIIVHLNESV KIECTRPNNK TRTSIRIGPG QWFYATGQVI GDIREAYCNI NES KWNETL QRVSKKLKEY FPHKNITFQP SSGGDLEITT HSFNCGGEFF YCNTSSLFNR TYMANSTDMA NSTETNSTRT ITIH CRIKQ IINMWQEVGR AMYAPPIAGN ITCISNITGL LLTRDGGKNN TETFRPGGGN MKDNWRSELY KYKVVKIEPL GVAPT RCKR RV

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Glycoprotein 41

MacromoleculeName: Glycoprotein 41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 18.146699 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GRRRRRRAVG IGAVFLGFLG AAGSTMGAAS MTLTVQARNL LSGIVQQQSN LLRAPEAQQH LLKLTVWGIK QLQARVLAVE RYLRDQQLL GIWGCSGKLI CCTNVPWNSS WSNRNLSEIW DNMTWLQWDK EISNYTQIIY GLLEESQNQQ EKNEQDLLAL D

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: CH235.12 Fab Heavy Chain

MacromoleculeName: CH235.12 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.319373 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVRLAQYGGG VKRLGATMTL SCVASGYTFN DYYIHWVRQA PGQGFELLGY IDPANGRPDY AGALRERLSF YRDKSMETLY MDLRSLRYD DTAMYYCVRN VGTAGSLLHY DHWGSGSPVI VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QVRLAQYGGG VKRLGATMTL SCVASGYTFN DYYIHWVRQA PGQGFELLGY IDPANGRPDY AGALRERLSF YRDKSMETLY MDLRSLRYD DTAMYYCVRN VGTAGSLLHY DHWGSGSPVI VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSC

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Macromolecule #4: CH235.12 Fab Light Chain

MacromoleculeName: CH235.12 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.450996 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPAT LSASPGERVT LTCRASRSVR NNVAWYQHKG GQSPRLLIYD ASTRAAGVPA RFSGSASGTE FTLAISNLES EDFTVYFCL QYNNWWTFGQ GTRVDIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
EIVLTQSPAT LSASPGERVT LTCRASRSVR NNVAWYQHKG GQSPRLLIYD ASTRAAGVPA RFSGSASGTE FTLAISNLES EDFTVYFCL QYNNWWTFGQ GTRVDIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 13 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #9: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 9 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose / Mannose

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Details: BLOT FOR 2.5 S BEFORE PLUNGING.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 93.15 K / Max: 93.15 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 66.71 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6uda

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 53398

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Atomic model buiding 1

Initial model
PDB IDChain

6uda

source_name: PDB, initial_model_type: experimental model

5f96

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-7tcn:
Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.SOSIP.664 with high-mannose glycans

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