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- PDB-8fr6: Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP -

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Basic information

Entry
Database: PDB / ID: 8fr6
TitleAntibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
Components
  • (Envelope glycoprotein ...) x 2
  • (vFP53.02 Fab ...) x 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / fusion peptide envelope trimer murine antibody vFP1 class / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / 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 / 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 / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / 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
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsWang, S. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J Virol / Year: 2023
Title: Diverse Murine Vaccinations Reveal Distinct Antibody Classes to Target Fusion Peptide and Variation in Peptide Length to Improve HIV Neutralization.
Authors: Mallika Sastry / Anita Changela / Jason Gorman / Kai Xu / Gwo-Yu Chuang / Chen-Hsiang Shen / Cheng Cheng / Hui Geng / Sijy O'Dell / Li Ou / Reda Rawi / Mateo Reveiz / Guillaume B E Stewart- ...Authors: Mallika Sastry / Anita Changela / Jason Gorman / Kai Xu / Gwo-Yu Chuang / Chen-Hsiang Shen / Cheng Cheng / Hui Geng / Sijy O'Dell / Li Ou / Reda Rawi / Mateo Reveiz / Guillaume B E Stewart-Jones / Shuishu Wang / Baoshan Zhang / Tongqing Zhou / Andrea Biju / Michael Chambers / Xuejun Chen / Angela R Corrigan / Bob C Lin / Mark K Louder / Krisha McKee / Alexandra F Nazzari / Adam S Olia / Danealle K Parchment / Edward K Sarfo / Tyler Stephens / Jonathan Stuckey / Yaroslav Tsybovsky / Raffaello Verardi / Yiran Wang / Cheng-Yan Zheng / Yuling Chen / Nicole A Doria-Rose / Adrian B McDermott / John R Mascola / Peter D Kwong /
Abstract: While neutralizing antibodies that target the HIV-1 fusion peptide have been elicited in mice by vaccination, antibodies reported thus far have been from only a single antibody class that could ...While neutralizing antibodies that target the HIV-1 fusion peptide have been elicited in mice by vaccination, antibodies reported thus far have been from only a single antibody class that could neutralize ~30% of HIV-1 strains. To explore the ability of the murine immune system to generate cross-clade neutralizing antibodies and to investigate how higher breadth and potency might be achieved, we tested 17 prime-boost regimens that utilized diverse fusion peptide-carrier conjugates and HIV-1 envelope trimers with different fusion peptides. We observed priming in mice with fusion peptide-carrier conjugates of variable peptide length to elicit higher neutralizing responses, a result we confirmed in guinea pigs. From vaccinated mice, we isolated 21 antibodies, belonging to 4 distinct classes of fusion peptide-directed antibodies capable of cross-clade neutralization. Top antibodies from each class collectively neutralized over 50% of a 208-strain panel. Structural analyses - both X-ray and cryo-EM - revealed each antibody class to recognize a distinct conformation of fusion peptide and to have a binding pocket capable of accommodating diverse fusion peptides. Murine vaccinations can thus elicit diverse neutralizing antibodies, and altering peptide length during prime can improve the elicitation of cross-clade responses targeting the fusion peptide site of HIV-1 vulnerability. The HIV-1 fusion peptide has been identified as a site for elicitation of broadly neutralizing antibodies, with prior studies demonstrating that priming with fusion peptide-based immunogens and boosting with soluble envelope (Env) trimers can elicit cross-clade HIV-1-neutralizing responses. To improve the neutralizing breadth and potency of fusion peptide-directed responses, we evaluated vaccine regimens that incorporated diverse fusion peptide-conjugates and Env trimers with variation in fusion peptide length and sequence. We found that variation in peptide length during prime elicits enhanced neutralizing responses in mice and guinea pigs. We identified vaccine-elicited murine monoclonal antibodies from distinct classes capable of cross-clade neutralization and of diverse fusion peptide recognition. Our findings lend insight into improved immunogens and regimens for HIV-1 vaccine development.
History
DepositionJan 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 7, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
A: Envelope glycoprotein gp41
B: Envelope glycoprotein gp41
C: Envelope glycoprotein gp120
F: Envelope glycoprotein gp41
G: Envelope glycoprotein gp120
I: Envelope glycoprotein gp120
D: vFP53.02 Fab heavy chain
E: vFP53.02 Fab light chain
H: vFP53.02 Fab heavy chain
L: vFP53.02 Fab light chain
J: vFP53.02 Fab heavy chain
K: vFP53.02 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,71375
Polymers356,48712
Non-polymers31,22663
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "F"
d_1ens_2chain "C"
d_2ens_2chain "G"
d_3ens_2chain "I"
d_1ens_3chain "D"
d_2ens_3chain "H"
d_3ens_3chain "J"
d_1ens_4chain "E"
d_2ens_4chain "K"
d_3ens_4chain "L"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAASPASPAA512 - 6641 - 153
d_12ens_1NAGNAGNAGNAGACB701
d_13ens_1NAGNAGNAGNAGADB702
d_14ens_1NAGNAGNAGNAGAEB703
d_21ens_1ALAALAASPASPBB512 - 6641 - 153
d_22ens_1NAGNAGNAGNAGBFB701
d_23ens_1NAGNAGNAGNAGBGB702
d_24ens_1NAGNAGNAGNAGBHB703
d_31ens_1ALAALAASPASPFD512 - 6641 - 153
d_32ens_1NAGNAGNAGNAGFMB701
d_33ens_1NAGNAGNAGNAGFNB702
d_34ens_1NAGNAGNAGNAGFOB703
d_11ens_2ALAALAVALVALCC31 - 5051 - 473
d_12ens_2NAGNAGNAGNAGCIB601
d_13ens_2NAGNAGNAGNAGCJB602
d_14ens_2NAGNAGNAGNAGCKB603
d_15ens_2NAGNAGNAGNAGCLB604
d_16ens_2NAGNAGNAGNAGMM1
d_17ens_2NAGNAGNAGNAGNN1
d_18ens_2BMABMABMABMANN3
d_19ens_2MANMANMANMANNN4
d_110ens_2BMABMABMABMARR3
d_111ens_2NAGNAGNAGNAGOO1
d_112ens_2NAGNAGNAGNAGPP1
d_113ens_2NAGNAGNAGNAGQQ1
d_114ens_2NAGNAGNAGNAGRR1
d_115ens_2BMABMABMABMAPP3
d_116ens_2NAGNAGNAGNAGSS1
d_117ens_2NAGNAGNAGNAGTT1
d_118ens_2BMABMABMABMAQQ3
d_119ens_2MANMANMANMANQQ4
d_120ens_2MANMANMANMANWW4
d_121ens_2NAGNAGNAGNAGUU1
d_122ens_2NAGNAGNAGNAGVV1
d_123ens_2BMABMABMABMARR3
d_124ens_2BMABMABMABMASS3
d_125ens_2BMABMABMABMAUU3
d_126ens_2BMABMABMABMAVV3
d_127ens_2NAGNAGNAGNAGWW1
d_128ens_2NAGNAGNAGNAGXX1
d_129ens_2BMABMABMABMAWW3
d_130ens_2NAGNAGNAGNAGYY1
d_131ens_2NAGNAGNAGNAGZZ1
d_132ens_2BMABMABMABMAXX3
d_133ens_2BMABMABMABMAYY3
d_134ens_2BMABMABMABMAZZ3
d_21ens_2ALAALAVALVALGE31 - 5051 - 473
d_22ens_2NAGNAGNAGNAGGPB601
d_23ens_2NAGNAGNAGNAGGQB602
d_24ens_2NAGNAGNAGNAGGRB603
d_25ens_2NAGNAGNAGNAGGSB604
d_26ens_2NAGNAGNAGNAGaAA1
d_27ens_2NAGNAGNAGNAGbBA1
d_28ens_2BMABMABMABMAbBA3
d_29ens_2MANMANMANMANbBA4
d_210ens_2MANMANMANMANeEA4
d_211ens_2NAGNAGNAGNAGcCA1
d_212ens_2NAGNAGNAGNAGdDA1
d_213ens_2NAGNAGNAGNAGeEA1
d_214ens_2NAGNAGNAGNAGfFA1
d_215ens_2BMABMABMABMAdDA3
d_216ens_2NAGNAGNAGNAGgGA1
d_217ens_2NAGNAGNAGNAGhHA1
d_218ens_2BMABMABMABMAeEA3
d_219ens_2MANMANMANMANkKA4
d_220ens_2NAGNAGNAGNAGiIA1
d_221ens_2NAGNAGNAGNAGjJA1
d_222ens_2BMABMABMABMAfFA3
d_223ens_2NAGNAGNAGNAGkKA1
d_224ens_2NAGNAGNAGNAGlLA1
d_225ens_2BMABMABMABMAgGA3
d_226ens_2NAGNAGNAGNAGmMA1
d_227ens_2NAGNAGNAGNAGnNA1
d_228ens_2BMABMABMABMAiIA3
d_229ens_2BMABMABMABMAjJA3
d_230ens_2BMABMABMABMAkKA3
d_231ens_2NAGNAGNAGNAGdDA1
d_232ens_2BMABMABMABMAlLA3
d_233ens_2BMABMABMABMAmMA3
d_234ens_2BMABMABMABMAnNA3
d_31ens_2ALAALAVALVALIF31 - 5051 - 473
d_32ens_2NAGNAGNAGNAGITB601
d_33ens_2NAGNAGNAGNAGIUB602
d_34ens_2NAGNAGNAGNAGIVB603
d_35ens_2NAGNAGNAGNAGIWB604
d_36ens_2NAGNAGNAGNAGoOA1
d_37ens_2NAGNAGNAGNAGpPA1
d_38ens_2BMABMABMABMApPA3
d_39ens_2MANMANMANMANpPA4
d_310ens_2MANMANMANMANsSA4
d_311ens_2NAGNAGNAGNAGqQA1
d_312ens_2NAGNAGNAGNAGrRA1
d_313ens_2NAGNAGNAGNAGsSA1
d_314ens_2NAGNAGNAGNAGtTA1
d_315ens_2BMABMABMABMArRA3
d_316ens_2NAGNAGNAGNAGuUA1
d_317ens_2NAGNAGNAGNAGvVA1
d_318ens_2BMABMABMABMAsSA3
d_319ens_2MANMANMANMANyYA4
d_320ens_2NAGNAGNAGNAGwWA1
d_321ens_2NAGNAGNAGNAGxXA1
d_322ens_2BMABMABMABMAtTA3
d_323ens_2NAGNAGNAGNAGyYA1
d_324ens_2NAGNAGNAGNAGzZA1
d_325ens_2BMABMABMABMAuUA3
d_326ens_2NAGNAGNAGNAG0AB1
d_327ens_2NAGNAGNAGNAG1BB1
d_328ens_2BMABMABMABMAwWA3
d_329ens_2BMABMABMABMAxXA3
d_330ens_2BMABMABMABMAyYA3
d_331ens_2BMABMABMABMAzZA3
d_332ens_2BMABMABMABMA0AB3
d_333ens_2BMABMABMABMA1BB3
d_11ens_3GLNGLNSERSERDG1 - 1131 - 118
d_21ens_3GLNGLNSERSERHI1 - 1131 - 118
d_31ens_3GLNGLNSERSERJK1 - 1131 - 118
d_11ens_4ASPASPARGARGEH1 - 1081 - 113
d_21ens_4ASPASPARGARGKL1 - 1081 - 113
d_31ens_4ASPASPARGARGLJ1 - 1081 - 113

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(-0.499567271435, -0.866274602138, -0.000924662924312), (0.866274863523, -0.499566071616, -0.00126527422016), (0.000634144696997, -0.00143310183835, 0.999998772039)440.018083562, 117.949539771, 0.156631568022
2given(-0.500797879604, 0.865563998105, 0.000670051159589), (-0.865564085033, -0.500798118409, 0.000243514636238), (0.000546337862099, -0.000458020605395, 0.999999745866)117.973168395, 439.921796244, -0.00638159711218
3given(-0.498873880149, -0.866674593517, 2.56552436596E-5), (0.866674516813, -0.498873848044, -0.000406995276174), (0.000365531195668, -0.000180804566725, 0.999999916848)439.827961493, 117.632391772, -0.0240219257163
4given(-0.499730787158, 0.866180766471, 0.000141994859414), (-0.866180764725, -0.49973080154, 9.38763552591E-5), (0.000152273098261, -7.60803110048E-5, 0.999999985512)117.774050664, 439.845265216, -0.00489042436544
5given(-0.498489745142, -0.866895583338, -0.000146889809275), (0.866895561007, -0.498489669994, -0.00036771799276), (0.000245550051286, -0.000310641772113, 0.999999921603)439.848844068, 117.518588214, 0.0151658557433
6given(-0.49932127453, 0.866416700218, 0.000605298216278), (-0.866416831024, -0.499321407611, 8.25856225369E-5), (0.00037379191994, -0.000483203804069, 0.999999813397)117.592778928, 439.815514339, 0.0566094773146
7given(-0.500517644952, 0.86572166182, 0.00284452932779), (-0.865643576088, -0.500421665654, -0.0154711254396), (-0.0119702243216, -0.0102059198094, 0.999876268811)117.544843527, 442.550722124, 4.06680508817
8given(-0.495968175606, -0.868221379833, -0.0143945957853), (0.868258017905, -0.496081561705, 0.00557660104282), (-0.0119826178095, -0.00973240655982, 0.999880841467)442.145460692, 115.777776008, 3.94250040288

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Components

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

#1: Protein Envelope glycoprotein gp41


Mass: 17162.525 Da / Num. of mol.: 3 / Mutation: BG505 DS-SOSIP construct
Source method: isolated from a genetically manipulated source
Details: from HIV-1 BG505 DS-SOSIP / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): CHO-DG44 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q2N0S7
#2: Protein Envelope glycoprotein gp120


Mass: 52986.969 Da / Num. of mol.: 3 / Mutation: BG505 DS-SOSIP construct
Source method: isolated from a genetically manipulated source
Details: from HIV-1 BG505 DS-SOSIP / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): CHO-DG44 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q2N0S6

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Antibody , 2 types, 6 molecules DHJELK

#3: Antibody vFP53.02 Fab heavy chain


Mass: 24566.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#4: Antibody vFP53.02 Fab light chain


Mass: 24112.863 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Sugars , 5 types, 63 molecules

#5: 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.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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.: 24
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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: 1072.964 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 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.: 21 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 interestY
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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of antibody Fab vFP53.02 with HIV-1 Env trimer BG505 DS-SOSIPCOMPLEX#1-#40MULTIPLE SOURCES
2HIV-1 Env trimer BG505 DS-SOSIPCOMPLEX#1-#21RECOMBINANT
3Antibody FabCOMPLEX#3-#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Human immunodeficiency virus 111676
33Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Cricetulus griseus (Chinese hamster)10029
33Homo sapiens (human)9606
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 54.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11874
Image scansWidth: 11520 / Height: 8184

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameVersionCategory
4cryoSPARC3.3CTF correction
7UCSF Chimera1.16model fitting
8Coot0.9.8.5model fitting
14PHENIX1.20.1-4487model refinement
15Coot0.9.8.5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 557806 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 90.14 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002821639
ELECTRON MICROSCOPYf_angle_d0.50529364
ELECTRON MICROSCOPYf_chiral_restr0.04043774
ELECTRON MICROSCOPYf_plane_restr0.00363504
ELECTRON MICROSCOPYf_dihedral_angle_d15.56018274
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BELECTRON MICROSCOPYNCS constraints0.000712483998074
ens_1d_3FELECTRON MICROSCOPYNCS constraints0.000699722377033
ens_2d_2GELECTRON MICROSCOPYNCS constraints0.000699669557511
ens_2d_3IELECTRON MICROSCOPYNCS constraints0.000710415911329
ens_3d_2HELECTRON MICROSCOPYNCS constraints0.000706946070952
ens_3d_3JELECTRON MICROSCOPYNCS constraints0.000699277888172
ens_4d_2KELECTRON MICROSCOPYNCS constraints0.000714023724399
ens_4d_3LELECTRON MICROSCOPYNCS constraints0.000701056155814

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