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- EMDB-23098: Cryo-EM structure of the VRC316 clinical trial, vaccine-elicited,... -

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Entry
Database: EMDB / ID: EMD-23098
TitleCryo-EM structure of the VRC316 clinical trial, vaccine-elicited, human antibody 316-310-1B11 in complex with an H2 CAN05 HA trimer
Map dataSharpened map
Sample
  • Complex: 316-310-1B11 Fab in complex with an H2 CAN05 HA trimer
    • Protein or peptide: 316-310-1B11 Light Chain
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: 316-310-1B11 Heavy Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVRC / IMMUNE SYSTEM / VRC316 / H2 / Fab / Flu / IMMUNE SYSTEM-Viral protein complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus / Homo sapiens (human) / Influenza A virus (A/Canada/720/2005(H2N2))
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsGorman J / Kwong PD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateSimons Foundation (SF349247) United States
CitationJournal: Nat Med / Year: 2022
Title: A single residue in influenza virus H2 hemagglutinin enhances the breadth of the B cell response elicited by H2 vaccination.
Authors: Sarah F Andrews / Julie E Raab / Jason Gorman / Rebecca A Gillespie / Crystal S F Cheung / Reda Rawi / Lauren Y Cominsky / Jeffrey C Boyington / Adrian Creanga / Chen-Hsiang Shen / Darcy R ...Authors: Sarah F Andrews / Julie E Raab / Jason Gorman / Rebecca A Gillespie / Crystal S F Cheung / Reda Rawi / Lauren Y Cominsky / Jeffrey C Boyington / Adrian Creanga / Chen-Hsiang Shen / Darcy R Harris / Adam S Olia / Alexandra F Nazzari / Tongqing Zhou / Katherine V Houser / Grace L Chen / John R Mascola / Barney S Graham / Masaru Kanekiyo / Julie E Ledgerwood / Peter D Kwong / Adrian B McDermott /
Abstract: Conserved epitopes on the influenza hemagglutinin (HA) stem are an attractive target for universal vaccine strategies as they elicit broadly neutralizing antibodies. Such antibody responses to stem- ...Conserved epitopes on the influenza hemagglutinin (HA) stem are an attractive target for universal vaccine strategies as they elicit broadly neutralizing antibodies. Such antibody responses to stem-specific epitopes have been extensively characterized for HA subtypes H1 and H5 in humans. H2N2 influenza virus circulated 50 years ago and represents a pandemic threat due to the lack of widespread immunity, but, unlike H1 and H5, the H2 HA stem contains Phe45 predicted to sterically clash with HA stem-binding antibodies characterized to date. To understand the effect of Phe45, we compared the HA stem-specific B cell response in post hoc analyses of two phase 1 clinical trials, one testing vaccination with an H2 ferritin nanoparticle immunogen ( NCT03186781 ) and one with an inactivated H5N1 vaccine ( NCT01086657 ). In H2-naive individuals, the magnitude of the B cell response was equivalent, but H2-elicited HA stem-binding B cells displayed greater cross-reactivity than those elicited by H5. However, in individuals with childhood H2 exposure, H5-elicited HA stem-binding B cells also displayed high cross-reactivity, suggesting recall of memory B cells formed 50 years ago. Overall, we propose that a one-residue difference on an HA immunogen can alter establishment and expansion of broadly neutralizing memory B cells. These data have implications for stem-based universal influenza vaccination strategies.
History
DepositionDec 11, 2020-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l0l
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23098.png

Downloads & links

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Map

FileDownload / File: emd_23098.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 346.56 Å		1.08 Å/pix.
x 320 pix.
= 346.56 Å		1.08 Å/pix.
x 320 pix.
= 346.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.5809768 - 2.9433746
Average (Standard dev.)0.0032906453 (±0.049003962)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 346.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0831.0831.083
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z346.560346.560346.560
α/β/γ90.00090.00090.000
start NX/NY/NZ799196
NX/NY/NZ149138117
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.5812.9430.003

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Supplemental data

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Mask #1

Fileemd_23098_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_23098_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: density modified map with resolve

Fileemd_23098_additional_2.map
Annotationdensity modified map with resolve
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_23098_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_23098_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Sample components

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Entire : 316-310-1B11 Fab in complex with an H2 CAN05 HA trimer

EntireName: 316-310-1B11 Fab in complex with an H2 CAN05 HA trimer
Components
  • Complex: 316-310-1B11 Fab in complex with an H2 CAN05 HA trimer
    • Protein or peptide: 316-310-1B11 Light Chain
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: 316-310-1B11 Heavy Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 316-310-1B11 Fab in complex with an H2 CAN05 HA trimer

SupramoleculeName: 316-310-1B11 Fab in complex with an H2 CAN05 HA trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus

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Macromolecule #1: 316-310-1B11 Light Chain

MacromoleculeName: 316-310-1B11 Light Chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.460025 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGDRAT LSCRASQSVP SSYLAWYRHK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFSLTISRVE PEDFAVYYC QQYGSSPYTF GRGTKLDIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVLTQSPGT LSLSPGDRAT LSCRASQSVP SSYLAWYRHK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFSLTISRVE PEDFAVYYC QQYGSSPYTF GRGTKLDIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #2: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Canada/720/2005(H2N2)) / Strain: A/Canada/720/2005(H2N2)
Molecular weightTheoretical: 38.802152 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAIIYLILLF TAVRGDQICI GYHANNSTEK VDTICERNVT VTHAKDILEK THNGKLCKLN GIPPLELGDC SIAGWLLGNP ECDRLLSVP EWSYIMEKEN PRDGLCYPGS FNDYEELKHL LSSVKHFEKV KILPKDRWTQ HTTTGGSRAC AVSGNPSFFR N MVWLTKKG ...String:
MAIIYLILLF TAVRGDQICI GYHANNSTEK VDTICERNVT VTHAKDILEK THNGKLCKLN GIPPLELGDC SIAGWLLGNP ECDRLLSVP EWSYIMEKEN PRDGLCYPGS FNDYEELKHL LSSVKHFEKV KILPKDRWTQ HTTTGGSRAC AVSGNPSFFR N MVWLTKKG SNYPVAQGSY NNTSGEQMLI IWGVHHPNDE TEQRTLYQNV GTYVSVGTST LNKRSTPEIA TRPKVNGQGG RM EFSWTLL DMWDTINFES TGNLIAPEYG FKISKRGSSG IMKTEGTLEN CETKCQTPLG AINTTLPFHN VHPLTIGECP KYV KSEKLV LATGLRNVPQ IESRRRRRR

UniProtKB: Hemagglutinin

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Macromolecule #3: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Canada/720/2005(H2N2)) / Strain: A/Canada/720/2005(H2N2)
Molecular weightTheoretical: 25.489357 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFGAIAGFI EGGWQGMVDG WYGYHHSNDQ GSGYAADKES TQKAFDCITN KVNSVIEKMN TQFEAVGKEF SNLERRLENL NKKMEDGFL DVWTYNAELL VLMENERTLD FHDSNVKNLY DKVRMQLRDN VKELGNGCFE FYHKCDDECM NSVKNGTYDY P KYEEESKL ...String:
GLFGAIAGFI EGGWQGMVDG WYGYHHSNDQ GSGYAADKES TQKAFDCITN KVNSVIEKMN TQFEAVGKEF SNLERRLENL NKKMEDGFL DVWTYNAELL VLMENERTLD FHDSNVKNLY DKVRMQLRDN VKELGNGCFE FYHKCDDECM NSVKNGTYDY P KYEEESKL NRNEIKGVKG RLVPRGSPGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGHH HHHH

UniProtKB: Hemagglutinin

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Macromolecule #4: 316-310-1B11 Heavy Chain

MacromoleculeName: 316-310-1B11 Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.065092 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKTSGGIFR SNAISWVRQA PGQGLEWMGG VVAIFGTTNY AQNFQGRVTI TADESSSTVY MELSRLRSE DTAVYYCARH SGYHITNTFF DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QVQLVQSGAE VKKPGSSVKV SCKTSGGIFR SNAISWVRQA PGQGLEWMGG VVAIFGTTNY AQNFQGRVTI TADESSSTVY MELSRLRSE DTAVYYCARH SGYHITNTFF DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKG LEVLFQGP

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / 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

Concentration2 mg/mL
BufferpH: 7.4 / Component - Formula: PBS
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
DetailsCryo-EM structure of the VRC316 clinical trial, vaccine-elicited, human antibody 316-310-1B11 in complex with an H2 CAN05 HA trimer

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2439 / Average electron dose: 51.16 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination 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

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 115194
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.12)

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Atomic model buiding 1

Initial modelPDB ID:

3ku3


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7l0l:
Cryo-EM structure of the VRC316 clinical trial, vaccine-elicited, human antibody 316-310-1B11 in complex with an H2 CAN05 HA trimer

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