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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: To Be Published
Title: Dual Vaccine Elicitation of HIV-1 Neutralizing Antibodies against V2 Apex and Fusion Peptide
Authors: Duan, H. / Nkolola, J.P. / Wang, S. / Kwong, P.D. / Barouch, D.H. / Zhou, T.
History
DepositionJul 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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