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- PDB-9pnn: Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-S... -

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Basic information

Entry
Database: PDB / ID: 9pnn
TitleCryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer
Components
  • (Envelope glycoprotein BG505 DS-SOSIP ...) x 2
  • (antibody J601-A6 ...) x 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody-antigen complex / fusion peptide directed / viral surface glycoprotein / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / 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 ...symbiont-mediated perturbation of host defense response / 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Macaca mulatta (Rhesus monkey)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang, S. / Zhou, T. / Kwong, P.D. / Morano, N.C. / Shapiro, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2026
Title: Vaccine elicitation of HIV-1 neutralizing antibodies against both V2 apex and fusion peptide in rhesus macaques.
Authors: Hongying Duan / Joseph P Nkolola / Shuishu Wang / Jayeshbhai Chaudhari / I-Ting Teng / Christy Lavine / Danealle K Parchment / George S Sellers / Krisha McKee / Sijy O'Dell / Misook Choe / ...Authors: Hongying Duan / Joseph P Nkolola / Shuishu Wang / Jayeshbhai Chaudhari / I-Ting Teng / Christy Lavine / Danealle K Parchment / George S Sellers / Krisha McKee / Sijy O'Dell / Misook Choe / Haijuan Du / Baoshan Zhang / Alejandro A Espinosa Perez / Annika Rossler / Ninaad Lasrado / Andrea Biju / Jordan E Becker / Robin Carroll / Audrey S Carson / Amy R Henry / Nicholas C Morano / Madeeha Mughal / Reda Rawi / Ryan S Roark / Chaim A Schramm / Chen-Hsiang Shen / Sarah C Smith / Tyler Stephens / Yaroslav Tsybovsky / David J Van Wazer / Hua Wang / Yongping Yang / Lucy Rutten / Johannes P M Langedijk / Cheng Cheng / Lingshu Wang / Daniel C Douek / Richard A Koup / John R Mascola / Lawrence Shapiro / Tongqing Zhou / Nicole A Doria-Rose / Bette Korber / Michael S Seaman / Theodore C Pierson / Peter D Kwong / Dan H Barouch /
Abstract: Broadly neutralizing antibodies (bNAbs) targeting multiple sites of HIV-1 Env vulnerability can be induced by infection, but simultaneous elicitation of bNAbs against multiple epitopes has not been ...Broadly neutralizing antibodies (bNAbs) targeting multiple sites of HIV-1 Env vulnerability can be induced by infection, but simultaneous elicitation of bNAbs against multiple epitopes has not been achieved by vaccination. In this study, we designed a dual-epitope vaccine targeting both the fusion peptide (FP) and the V2 apex and evaluated its capacity to induce bNAbs against both epitopes in rhesus macaques. This vaccine combined an FP conjugate with a cocktail of engineered Env trimers with enhanced V2 apex recognition and increased antigen retention in lymph nodes. Macaque immunization with the dual-epitope vaccine elicited >1,000-fold higher autologous tier 2-neutralizing titers than wild-type Env trimers and enhanced heterologous neutralization. Both FP- and V2 apex-monoclonal antibodies were isolated from immunized macaques and showed heterologous neutralization with genetic and structural signatures similar to well-characterized FP and V2 apex bNAbs. These results demonstrate proof of concept for simultaneous vaccine elicitation of neutralizing antibodies against multiple sites of Env vulnerability.
History
DepositionJul 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Envelope glycoprotein BG505 DS-SOSIP gp41
G: Envelope glycoprotein BG505 DS-SOSIP gp120
H: antibody J601-A6 heavy chain
L: antibody J601-A6 light chain
A: Envelope glycoprotein BG505 DS-SOSIP gp41
C: Envelope glycoprotein BG505 DS-SOSIP gp120
D: antibody J601-A6 heavy chain
E: antibody J601-A6 light chain
F: Envelope glycoprotein BG505 DS-SOSIP gp41
I: Envelope glycoprotein BG505 DS-SOSIP gp120
J: antibody J601-A6 heavy chain
K: antibody J601-A6 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,17472
Polymers356,51612
Non-polymers31,65860
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "F"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_1ens_2chain "G"
d_2ens_2chain "C"
d_3ens_2chain "I"
d_1ens_3chain "J"
d_2ens_3chain "H"
d_3ens_3chain "D"
d_1ens_4chain "L"
d_2ens_4chain "K"
d_3ens_4chain "E"

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_1ALAALAASPASPFI512 - 6641 - 153
d_12ens_1NAGNAGNAGNAGFPB701
d_13ens_1NAGNAGNAGNAGFQB702
d_21ens_1ALAALAASPASPBA512 - 6641 - 153
d_22ens_1NAGNAGNAGNAGBFB701
d_23ens_1NAGNAGNAGNAGBGB702
d_31ens_1ALAALAASPASPAE512 - 6641 - 153
d_32ens_1NAGNAGNAGNAGAKB701
d_33ens_1NAGNAGNAGNAGALB702
d_11ens_2ALAALAVALVALGB31 - 5051 - 473
d_12ens_2NAGNAGNAGNAGMM1
d_13ens_2NAGNAGNAGNAGMM2
d_14ens_2BMABMABMABMAMM3
d_15ens_2MANMANMANMANMM4
d_16ens_2NAGNAGNAGNAGNN1
d_17ens_2NAGNAGNAGNAGNN2
d_18ens_2NAGNAGNAGNAGGHB601
d_19ens_2NAGNAGNAGNAGOO1
d_110ens_2NAGNAGNAGNAGOO2
d_111ens_2BMABMABMABMAOO3
d_112ens_2MANMANMANMANOO4
d_113ens_2MANMANMANMANOO5
d_114ens_2NAGNAGNAGNAGPP1
d_115ens_2NAGNAGNAGNAGPP2
d_116ens_2NAGNAGNAGNAGQQ1
d_117ens_2NAGNAGNAGNAGQQ2
d_118ens_2BMABMABMABMAQQ3
d_119ens_2NAGNAGNAGNAGRR1
d_120ens_2NAGNAGNAGNAGRR2
d_121ens_2BMABMABMABMARR3
d_122ens_2MANMANMANMANRR4
d_123ens_2MANMANMANMANRR5
d_124ens_2MANMANMANMANRR6
d_125ens_2NAGNAGNAGNAGSS1
d_126ens_2NAGNAGNAGNAGSS2
d_127ens_2BMABMABMABMASS3
d_128ens_2NAGNAGNAGNAGTT1
d_129ens_2NAGNAGNAGNAGTT2
d_130ens_2BMABMABMABMATT3
d_131ens_2NAGNAGNAGNAGUU1
d_132ens_2NAGNAGNAGNAGUU2
d_133ens_2NAGNAGNAGNAGVV1
d_134ens_2NAGNAGNAGNAGVV2
d_135ens_2BMABMABMABMAVV3
d_136ens_2NAGNAGNAGNAGWW1
d_137ens_2NAGNAGNAGNAGWW2
d_138ens_2BMABMABMABMAWW3
d_139ens_2NAGNAGNAGNAGXX1
d_140ens_2NAGNAGNAGNAGXX2
d_141ens_2BMABMABMABMAXX3
d_142ens_2MANMANMANMANXX4
d_143ens_2NAGNAGNAGNAGYY1
d_144ens_2NAGNAGNAGNAGYY2
d_145ens_2BMABMABMABMAYY3
d_146ens_2NAGNAGNAGNAGZZ1
d_147ens_2NAGNAGNAGNAGZZ2
d_148ens_2BMABMABMABMAZZ3
d_149ens_2NAGNAGNAGNAGGIB602
d_150ens_2NAGNAGNAGNAGGJB603
d_151ens_2NAGNAGNAGNAGaAA1
d_152ens_2NAGNAGNAGNAGaAA2
d_153ens_2BMABMABMABMAaAA3
d_21ens_2ALAALAVALVALCF31 - 5051 - 473
d_22ens_2NAGNAGNAGNAGbBA1
d_23ens_2NAGNAGNAGNAGbBA2
d_24ens_2BMABMABMABMAbBA3
d_25ens_2MANMANMANMANbBA4
d_26ens_2NAGNAGNAGNAGcCA1
d_27ens_2NAGNAGNAGNAGcCA2
d_28ens_2NAGNAGNAGNAGCMB601
d_29ens_2NAGNAGNAGNAGdDA1
d_210ens_2NAGNAGNAGNAGdDA2
d_211ens_2BMABMABMABMAdDA3
d_212ens_2MANMANMANMANdDA4
d_213ens_2MANMANMANMANdDA5
d_214ens_2NAGNAGNAGNAGeEA1
d_215ens_2NAGNAGNAGNAGeEA2
d_216ens_2NAGNAGNAGNAGfFA1
d_217ens_2NAGNAGNAGNAGfFA2
d_218ens_2BMABMABMABMAfFA3
d_219ens_2NAGNAGNAGNAGgGA1
d_220ens_2NAGNAGNAGNAGgGA2
d_221ens_2BMABMABMABMAgGA3
d_222ens_2MANMANMANMANgGA4
d_223ens_2MANMANMANMANgGA5
d_224ens_2MANMANMANMANgGA6
d_225ens_2NAGNAGNAGNAGhHA1
d_226ens_2NAGNAGNAGNAGhHA2
d_227ens_2BMABMABMABMAhHA3
d_228ens_2NAGNAGNAGNAGiIA1
d_229ens_2NAGNAGNAGNAGiIA2
d_230ens_2BMABMABMABMAiIA3
d_231ens_2NAGNAGNAGNAGjJA1
d_232ens_2NAGNAGNAGNAGjJA2
d_233ens_2NAGNAGNAGNAGkKA1
d_234ens_2NAGNAGNAGNAGkKA2
d_235ens_2BMABMABMABMAkKA3
d_236ens_2NAGNAGNAGNAGlLA1
d_237ens_2NAGNAGNAGNAGlLA2
d_238ens_2BMABMABMABMAlLA3
d_239ens_2NAGNAGNAGNAGmMA1
d_240ens_2NAGNAGNAGNAGmMA2
d_241ens_2BMABMABMABMAmMA3
d_242ens_2MANMANMANMANmMA4
d_243ens_2NAGNAGNAGNAGnNA1
d_244ens_2NAGNAGNAGNAGnNA2
d_245ens_2BMABMABMABMAnNA3
d_246ens_2NAGNAGNAGNAGoOA1
d_247ens_2NAGNAGNAGNAGoOA2
d_248ens_2BMABMABMABMAoOA3
d_249ens_2NAGNAGNAGNAGCNB602
d_250ens_2NAGNAGNAGNAGCOB603
d_251ens_2NAGNAGNAGNAGpPA1
d_252ens_2NAGNAGNAGNAGpPA2
d_253ens_2BMABMABMABMApPA3
d_31ens_2ALAALAVALVALIJ31 - 5051 - 473
d_32ens_2NAGNAGNAGNAGqQA1
d_33ens_2NAGNAGNAGNAGqQA2
d_34ens_2BMABMABMABMAqQA3
d_35ens_2MANMANMANMANqQA4
d_36ens_2NAGNAGNAGNAGrRA1
d_37ens_2NAGNAGNAGNAGrRA2
d_38ens_2NAGNAGNAGNAGIRB601
d_39ens_2NAGNAGNAGNAGsSA1
d_310ens_2NAGNAGNAGNAGsSA2
d_311ens_2BMABMABMABMAsSA3
d_312ens_2MANMANMANMANsSA4
d_313ens_2MANMANMANMANsSA5
d_314ens_2NAGNAGNAGNAGtTA1
d_315ens_2NAGNAGNAGNAGtTA2
d_316ens_2NAGNAGNAGNAGuUA1
d_317ens_2NAGNAGNAGNAGuUA2
d_318ens_2BMABMABMABMAuUA3
d_319ens_2NAGNAGNAGNAGvVA1
d_320ens_2NAGNAGNAGNAGvVA2
d_321ens_2BMABMABMABMAvVA3
d_322ens_2MANMANMANMANvVA4
d_323ens_2MANMANMANMANvVA5
d_324ens_2MANMANMANMANvVA6
d_325ens_2NAGNAGNAGNAGwWA1
d_326ens_2NAGNAGNAGNAGwWA2
d_327ens_2BMABMABMABMAwWA3
d_328ens_2NAGNAGNAGNAGxXA1
d_329ens_2NAGNAGNAGNAGxXA2
d_330ens_2BMABMABMABMAxXA3
d_331ens_2NAGNAGNAGNAGyYA1
d_332ens_2NAGNAGNAGNAGyYA2
d_333ens_2NAGNAGNAGNAGzZA1
d_334ens_2NAGNAGNAGNAGzZA2
d_335ens_2BMABMABMABMAzZA3
d_336ens_2NAGNAGNAGNAG0AB1
d_337ens_2NAGNAGNAGNAG0AB2
d_338ens_2BMABMABMABMA0AB3
d_339ens_2NAGNAGNAGNAG1BB1
d_340ens_2NAGNAGNAGNAG1BB2
d_341ens_2BMABMABMABMA1BB3
d_342ens_2MANMANMANMAN1BB4
d_343ens_2NAGNAGNAGNAG2CB1
d_344ens_2NAGNAGNAGNAG2CB2
d_345ens_2BMABMABMABMA2CB3
d_346ens_2NAGNAGNAGNAG3DB1
d_347ens_2NAGNAGNAGNAG3DB2
d_348ens_2BMABMABMABMA3DB3
d_349ens_2NAGNAGNAGNAGISB602
d_350ens_2NAGNAGNAGNAGITB603
d_351ens_2NAGNAGNAGNAG4EB1
d_352ens_2NAGNAGNAGNAG4EB2
d_353ens_2BMABMABMABMA4EB3
d_11ens_3GLNGLNSERSERJK1 - 1131 - 122
d_21ens_3GLNGLNSERSERHC1 - 1131 - 122
d_31ens_3GLNGLNSERSERDG1 - 1131 - 122
d_11ens_4ASPASPLYSLYSLD1 - 1072 - 108
d_21ens_4ASPASPLYSLYSKL1 - 1072 - 108
d_31ens_4ASPASPLYSLYSEH1 - 1072 - 108

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(-0.499953517572, 0.866052230777, -0.000117616122058), (-0.866052237312, -0.499953519986, 9.99593563328E-6), (-5.01455918761E-5, 0.000106859208834, 0.999999993033)117.879857462, 439.889370129, -0.00884423987748
2given(-0.500031229282, -0.866007371748, -4.26717154466E-5), (0.866007371237, -0.500031230733, 3.54315544502E-5), (-5.20211777386E-5, -1.9237136393E-5, 0.999999998462)439.906731642, 117.870587798, 0.0122021872527
3given(-0.499984931258, 0.866034095632, -0.000117124164988), (-0.866034097909, -0.499984938866, -4.65405404003E-5), (-9.88660132871E-5, 7.81639516758E-5, 0.999999992058)117.891177707, 439.901412952, 0.000201202538591
4given(-0.499947404552, -0.866055767647, -2.88124229573E-6), (0.866055764086, -0.499947402792, 8.90799129077E-5), (-7.85886419578E-5, 4.20399547579E-5, 0.999999996028)439.891677475, 117.834680136, 0.00487712083296
5given(-0.499917038463, 0.866073280755, -0.000164368641156), (-0.86607329593, -0.499917023293, 0.000126091643828), (2.70339218369E-5, 0.000205390651951, 0.999999978542)117.880040175, 439.869174142, -0.0360123920285
6given(-0.499977278819, -0.866038519076, 6.43573327647E-5), (0.866038521464, -0.499977277642, 3.43867289611E-5), (2.39697220671E-6, 7.29285124864E-5, 0.999999997338)439.885160528, 117.856568521, -0.00945625352222
7given(-0.500003262601, -0.866023501668, -0.000178735036769), (0.86602350904, -0.500003278562, 5.67132695928E-5), (-0.000138483128702, -0.000126431923902, 0.999999982419)439.923249015, 117.859021475, 0.053075315419
8given(-0.499788103153, 0.866147707096, 3.79383904974E-5), (-0.866147674983, -0.499788095745, 0.000253913611521), (0.000238887848362, 9.4042753545E-5, 0.999999967044)117.799021524, 439.829166368, -0.0675599794264

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Components

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Envelope glycoprotein BG505 DS-SOSIP ... , 2 types, 6 molecules BAFGCI

#1: Protein Envelope glycoprotein BG505 DS-SOSIP gp41


Mass: 17162.525 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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 BG505 DS-SOSIP gp120


Mass: 52986.969 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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 HDJLEK

#3: Antibody antibody J601-A6 heavy chain


Mass: 25058.914 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#4: Antibody antibody J601-A6 light chain


Mass: 23630.109 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)

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Sugars , 7 types, 60 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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
#7: 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-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
#8: 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
#9: 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
#10: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#11: 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: obtained synthetically / 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: HIV-1 Env BG505 DS-SOSIP in complex with antibody Fab / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293F
Buffer solutionpH: 7.4 / Details: PBS + 0.005% (w/v) DDM
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS 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: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
4cryoSPARC4.2.1CTF correction
7UCSF ChimeraX1.8model fitting
9UCSF ChimeraX1.8initial Euler assignment
11cryoSPARC4.2.1classification
12cryoSPARC4.2.13D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46939 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 123.2 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00221639
ELECTRON MICROSCOPYf_angle_d0.518229397
ELECTRON MICROSCOPYf_chiral_restr0.04273771
ELECTRON MICROSCOPYf_plane_restr0.00293516
ELECTRON MICROSCOPYf_dihedral_angle_d6.09345514
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2IFELECTRON MICROSCOPYNCS constraints3.45920469421E-12
ens_1d_3IFELECTRON MICROSCOPYNCS constraints7.88253676529E-13
ens_2d_2BGELECTRON MICROSCOPYNCS constraints1.29394216784E-11
ens_2d_3BGELECTRON MICROSCOPYNCS constraints1.23248469352E-10
ens_3d_2KJELECTRON MICROSCOPYNCS constraints6.66544897523E-12
ens_3d_3KJELECTRON MICROSCOPYNCS constraints2.54199897961E-12
ens_4d_2DLELECTRON MICROSCOPYNCS constraints1.5191398975E-13
ens_4d_3DLELECTRON MICROSCOPYNCS constraints2.62070051078E-12

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