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- EMDB-27622: Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSI... -

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Basic information

Entry
Database: EMDB / ID: EMD-27622
TitleVaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSIP.664.v4.1 Trimer, 2-Fab-bound configuration
Map dataSharp map from homogeneous C1 refinement in cryosparc
Sample
  • Organelle or cellular component: Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSIP.664.v4.1. Trimer, 2-Fab-bound configuration
    • Other: CH505TFchim.6R.SOSIP.664.V4.1 Env Trimer
    • Other: DH1285 Fab Heavy Chain
    • Other: DH1285 Fab Light Chain
KeywordsAntibody / IgG / HIV-1 / CD4 binding site / gp120 / Env / Fab / DH1285 / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsStalls V / Achyara P
Funding support United States, 2 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)UM1 AI144371 United States
CitationJournal: To be published
Title: Rhesus macaque vaccine elicited antibody DH1285 bound to HIV-1 Env trimer
Authors: Stalls V / Acharya P
History
DepositionJul 14, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27622.png

Downloads & links

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Map

FileDownload / File: emd_27622.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharp map from homogeneous C1 refinement in cryosparc
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: 0.916
Minimum - Maximum-0.51273274 - 2.543432
Average (Standard dev.)0.004653247 (±0.122340955)
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: Half B map from homogeneous C1 refinement in cryosparc

Fileemd_27622_half_map_1.map
AnnotationHalf B map from homogeneous C1 refinement in cryosparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A map from homogeneous C1 refinement in cryosparc

Fileemd_27622_half_map_2.map
AnnotationHalf A map from homogeneous C1 refinement in cryosparc
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSI...

EntireName: Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSIP.664.v4.1. Trimer, 2-Fab-bound configuration
Components
  • Organelle or cellular component: Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSIP.664.v4.1. Trimer, 2-Fab-bound configuration
    • Other: CH505TFchim.6R.SOSIP.664.V4.1 Env Trimer
    • Other: DH1285 Fab Heavy Chain
    • Other: DH1285 Fab Light Chain

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Supramolecule #1: Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSI...

SupramoleculeName: Vaccine Elicited Antibody DH1285 Fab bound to CH505TFchim.6R.SOSIP.664.v4.1. Trimer, 2-Fab-bound configuration
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 308 KDa

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Macromolecule #1: CH505TFchim.6R.SOSIP.664.V4.1 Env Trimer

MacromoleculeName: CH505TFchim.6R.SOSIP.664.V4.1 Env Trimer / type: other / ID: 1 / Classification: other
Source (natural)Organism: Human immunodeficiency virus 1
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAAENLWV TVYYGVPVWK EAKTTLFCAS DAKAYEKKVH NVWATHACVP TDPNPQEMVL KNVTENFNMW KNDMVDQMHE DVISLWDQSL KPCVKLTPLC VTLNCTNATA SNSSIIEGMK NCSFNITTEL RDKREKKNAL FYKLDIVQLD ...String:
MPMGSLQPLA TLYLLGMLVA SVLAAENLWV TVYYGVPVWK EAKTTLFCAS DAKAYEKKVH NVWATHACVP TDPNPQEMVL KNVTENFNMW KNDMVDQMHE DVISLWDQSL KPCVKLTPLC VTLNCTNATA SNSSIIEGMK NCSFNITTEL RDKREKKNAL FYKLDIVQLD GNSSQYRLIN CNTSVITQAC PKVSFDPIPI HYCAPAGYAI LKCNNKTFTG TGPCNNVSTV QCTHGIKPVV STQLLLNGSL AEGEIIIRSE NITNNVKTII VHLNESVKIE CTRPNNKTRT SIRIGPGQWF YATGQVIGDI REAYCNINES KWNETLQRVS KKLKEYFPHK NITFQPSSGG DLEITTHSFN CGGEFFYCNT SSLFNRTYMA NSTDMANSTE TNSTRTITIH CRIKQIINMW QEVGRAMYAP PIAGNITCIS NITGLLLTRD GGKNNTETFR PGGGNMKDNW RSELYKYKVV KIEPLGVAPT RCKRRVVGRR RRRRAVGIGA VFLGFLGAAG STMGAASMTL TVQARNLLSG IVQQQSNLLR APEAQQHLLK LTVWGIKQLQ ARVLAVERYL RDQQLLGIWG CSGKLICCTN VPWNSSWSNR NLSEIWDNMT WLQWDKEISN YTQIIYGLLE ESQNQQEKNE QDLLALD
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #2: DH1285 Fab Heavy Chain

MacromoleculeName: DH1285 Fab Heavy Chain / type: other / ID: 2 / Classification: other
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
SequenceString: MGWSCIILFL VATATGVHAQ VHLEQSGAEV KEPGSSVRLS CEASGYTFTD YYIHWVRQSP RQGLEWMGWI NPYYGNTHYA EKFQGRVAMT RDRSTTTAYM DLSSLTSEDT AVYYCARDEG GSGSYSYFDS WGQGVLVTVS SASTKGPSVF PLAPSSRSTS ESTAALGCLV ...String:
MGWSCIILFL VATATGVHAQ VHLEQSGAEV KEPGSSVRLS CEASGYTFTD YYIHWVRQSP RQGLEWMGWI NPYYGNTHYA EKFQGRVAMT RDRSTTTAYM DLSSLTSEDT AVYYCARDEG GSGSYSYFDS WGQGVLVTVS SASTKGPSVF PLAPSSRSTS ESTAALGCLV KDYFPEPVTV SWNSGSLTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYVCNVNHKP SNTKVDKRVE IKT
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #3: DH1285 Fab Light Chain

MacromoleculeName: DH1285 Fab Light Chain / type: other / ID: 3 / Classification: other
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
SequenceString: MGWSCIILFL VATATGVHAD IQMTQSPSSL SASVGDTVTI TCRASQDINN HLSWYQQKPG RAPKALIYSA SSLETGVPSR FSGSGSGTDY TLTISSLQPE DFATYYCQHY STSPYTFGRG TKVDIKRAVA APSVFIFPPS EDQVKSGTVS VVCLLNNFYP REASVKWKVD ...String:
MGWSCIILFL VATATGVHAD IQMTQSPSSL SASVGDTVTI TCRASQDINN HLSWYQQKPG RAPKALIYSA SSLETGVPSR FSGSGSGTDY TLTISSLQPE DFATYYCQHY STSPYTFGRG TKVDIKRAVA APSVFIFPPS EDQVKSGTVS VVCLLNNFYP REASVKWKVD GVLKTGNSQE SVTEQDSKDN TYSLSSTLTL SSTDYQSHNV YACEVTHQGL SSPVTKSFNR GEC
Recombinant expressionOrganism: Homo sapiens (human)

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4146196
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: UCSF ChimeraX / Number images used: 78101
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL

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