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- PDB-7uoj: The CryoEM structure of N49-P9.6-FR3 and PGT121 Fabs in complex w... -

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Entry
Database: PDB / ID: 7uoj
TitleThe CryoEM structure of N49-P9.6-FR3 and PGT121 Fabs in complex with BG505 SOSIP.664
Components
  • (Envelope glycoprotein ...) x 2
  • (N49-P9.6-FR3 Fab ...) x 2
  • PGT121 Fab heavy chain
  • PGT121 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / envelope trimer / GP120 / GP41 / viral entry / type-1 membrane fusion glycoprotein / N49P9.6-FR3 / PGT121 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / identical protein binding / 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
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.02 Å
AuthorsNguyen, D.N. / Tolbert, W.D. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI147870 United States
CitationJournal: To Be Published
Title: The structure of N49-P9.6-FR3 and PGT121 Fabs in complex with BG505 SOSIP
Authors: Nguyen, D.N. / Tolbert, W.D. / Pazgier, M.
History
DepositionApr 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 2.0Mar 13, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_software / pdbx_branch_scheme / pdbx_contact_author / pdbx_entity_branch_descriptor / pdbx_nonpoly_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine_ls_restr / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.chain_id / _em_3d_fitting_list.chain_residue_range / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.auth_seq_num / _pdbx_entity_branch_descriptor.descriptor / _pdbx_nonpoly_scheme.auth_seq_num / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _struct_mon_prot_cis.pdbx_omega_angle
Description: Ligand geometry
Details: NAG 1 chain W, NAG 1 chain n, and NAG 1 chain y were not correctly linked to Asn 276 on chains G, A, and I respectively. We refit the glycans of chains W, n, and y to fit the map and make ...Details: NAG 1 chain W, NAG 1 chain n, and NAG 1 chain y were not correctly linked to Asn 276 on chains G, A, and I respectively. We refit the glycans of chains W, n, and y to fit the map and make the correct bond link to the corresponding asparagines.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Envelope glycoprotein gp120
B: Envelope glycoprotein gp41
H: N49-P9.6-FR3 Fab heavy chain
L: N49-P9.6-FR3 Fab light chain
l: PGT121 Fab light chain
h: PGT121 Fab heavy chain
A: Envelope glycoprotein gp120
C: Envelope glycoprotein gp41
D: N49-P9.6-FR3 Fab heavy chain
E: N49-P9.6-FR3 Fab light chain
e: PGT121 Fab light chain
d: PGT121 Fab heavy chain
I: Envelope glycoprotein gp120
J: Envelope glycoprotein gp41
K: N49-P9.6-FR3 Fab heavy chain
M: N49-P9.6-FR3 Fab light chain
m: PGT121 Fab light chain
k: PGT121 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)521,66766
Polymers498,02018
Non-polymers23,64748
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Envelope glycoprotein ... , 2 types, 6 molecules GAIBCJ

#1: Protein Envelope glycoprotein gp120


Mass: 54064.277 Da / Num. of mol.: 3 / Mutation: T330N,A498C
Source method: isolated from a genetically manipulated source
Details: Env mimic BG505 SOSIP.664 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell (production host): HEK GnT1- 293 cells / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#2: Protein Envelope glycoprotein gp41 / Env polyprotein


Mass: 17146.482 Da / Num. of mol.: 3 / Fragment: UNP residues 509-661 / Mutation: I556P,T602C
Source method: isolated from a genetically manipulated source
Details: Env mimic BG505 SOSIP.664 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell (production host): HEK Gnt1- 293 cells / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6

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Antibody , 4 types, 12 molecules HDKLEMlemhdk

#3: Antibody N49-P9.6-FR3 Fab heavy chain


Mass: 25024.129 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 cells / Production host: Homo sapiens (human)
#4: Antibody N49-P9.6-FR3 Fab light chain


Mass: 21733.291 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 cells / Production host: Homo sapiens (human)
#5: Antibody PGT121 Fab light chain


Mass: 22869.338 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 cells / Production host: Homo sapiens (human)
#6: Antibody PGT121 Fab heavy chain


Mass: 25169.230 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 cells / Production host: Homo sapiens (human)

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Sugars , 6 types, 48 molecules

#7: Polysaccharide...
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#9: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#10: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#11: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#12: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: One BG505 SOSIP.644 trimer in complex with three N49-P9.6-FR3 Fabs and three PGT121 Fabs.
Type: COMPLEX
Details: Fab fragments were generated from papain digest of their respective IgGs. Each component was purified separately. Components were mixed and the complex was purified by gel filtration.
Entity ID: #1-#6 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Human immunodeficiency virus 111676
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2 / Details: Phosphate buffered saline
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Quantifoil R1.2/1.3
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 2700 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 58.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4368

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Processing

EM software
IDNameCategoryDetails
1cryoSPARCparticle selection
2SerialEMimage acquisitionused to collect micrographs
3cryoSPARCimage acquisitionused to select particles
5cryoSPARCCTF correction
8UCSF ChimeraXmodel fitting
10UCSF ChimeraXinitial Euler assignment
11PHENIXfinal Euler assignment
12cryoSPARCclassification
13PHENIX3D reconstruction
14PHENIXmodel refinement
Image processingDetails: Data sets from two grid types were combined into a single data set.
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 3151423
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132055 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDChain residue rangeInitial refinement model-IDPdb chain residue range
16CDI

6cdi

G6CDIG31-505131-505
26CDI

6cdi

A6CDIA31-505131-505
36CDI

6cdi

I6CDII31-505131-505
46CDI

6cdi

B6CDIB513-6641513-664
56CDI

6cdi

C6CDIC513-6641513-664
66CDI

6cdi

J6CDIJ513-6641513-664
75CEZ

5cez

h5CEZh1-11221-112
85CEZ

5cez

d5CEZd1-11221-112
95CEZ

5cez

k5CEZk1-11221-112
105CEZ

5cez

l5CEZl6-10726-107
115CEZ

5cez

e5CEZe6-10726-107
125CEZ

5cez

m5CEZm6-10726-107
137SX7

7sx7

H7SX7H1-11231-112
147SX7

7sx7

D7SX7D1-11231-112
157SX7

7sx7

K7SX7K1-11231-112
167SX7

7sx7

L7SX7L3-10733-107
177SX7

7sx7

E7SX7E3-10733-107
187SX7

7sx7

M7SX7M3-10733-107
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00426700
ELECTRON MICROSCOPYf_angle_d0.68736282
ELECTRON MICROSCOPYf_dihedral_angle_d9.364257
ELECTRON MICROSCOPYf_chiral_restr0.0544356
ELECTRON MICROSCOPYf_plane_restr0.0054482

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