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- PDB-8tox: Cryo-EM structure of BG505 Env mutant A517E in complex with antib... -

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Basic information

Entry
Database: PDB / ID: 8tox
TitleCryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab
Components
  • (Envelope glycoprotein ...) x 2
  • (antibody ACS202 Fab ...) x 2
KeywordsVIRAL PROTEIN/ANTIVIRAL PROTEIN / IMMUNE SYSTEM / complex / viral antigen / antibody / VIRAL PROTEIN / VIRAL PROTEIN-ANTIVIRAL 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: 2.3 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: Front Immunol / Year: 2024
Title: Vaccine-elicited and naturally elicited antibodies differ in their recognition of the HIV-1 fusion peptide.
Authors: Mateo Reveiz / Kai Xu / Myungjin Lee / Shuishu Wang / Adam S Olia / Darcy R Harris / Kevin Liu / Tracy Liu / Andrew J Schaub / Tyler Stephens / Yiran Wang / Baoshan Zhang / Rick Huang / ...Authors: Mateo Reveiz / Kai Xu / Myungjin Lee / Shuishu Wang / Adam S Olia / Darcy R Harris / Kevin Liu / Tracy Liu / Andrew J Schaub / Tyler Stephens / Yiran Wang / Baoshan Zhang / Rick Huang / Yaroslav Tsybovsky / Peter D Kwong / Reda Rawi /
Abstract: Broadly neutralizing antibodies have been proposed as templates for HIV-1 vaccine design, but it has been unclear how similar vaccine-elicited antibodies are to their naturally elicited templates. To ...Broadly neutralizing antibodies have been proposed as templates for HIV-1 vaccine design, but it has been unclear how similar vaccine-elicited antibodies are to their naturally elicited templates. To provide insight, here we compare the recognition of naturally elicited and vaccine-elicited antibodies targeting the HIV-1 fusion peptide, which comprises envelope (Env) residues 512-526, with the most common sequence being AVGIGAVFLGFLGAA. Naturally elicited antibodies bound peptides with substitutions to negatively charged amino acids at residue positions 517-520 substantially better than the most common sequence, despite these substitutions rarely appearing in HIV-1; by contrast, vaccine-elicited antibodies were less tolerant of sequence variation, with no substitution of residues 512-516 showing increased binding. Molecular dynamics analysis and cryo-EM structural analysis of the naturally elicited ACS202 antibody in complex with the HIV-1 Env trimer with an alanine 517 to glutamine substitution suggested enhanced binding to result from electrostatic interactions with positively charged antibody residues. Overall, vaccine-elicited antibodies appeared to be more fully optimized to bind the most common fusion peptide sequence, perhaps reflecting the immunization with fusion peptide of the vaccine-elicited antibodies.
History
DepositionAug 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: 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 gp41
G: Envelope glycoprotein gp120
A: Envelope glycoprotein gp41
C: Envelope glycoprotein gp120
F: Envelope glycoprotein gp41
I: Envelope glycoprotein gp120
H: antibody ACS202 Fab heavy chain
L: antibody ACS202 Fab light chain
D: antibody ACS202 Fab heavy chain
E: antibody ACS202 Fab light chain
J: antibody ACS202 Fab heavy chain
K: antibody ACS202 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,08375
Polymers357,48812
Non-polymers31,59563
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
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_1ALAALAASPASPAC512 - 6641 - 153
d_12ens_1NAGNAGNAGNAGdDA1
d_13ens_1NAGNAGNAGNAGdDA2
d_14ens_1NAGNAGNAGNAGAPB701
d_15ens_1NAGNAGNAGNAGeEA1
d_16ens_1NAGNAGNAGNAGeEA2
d_21ens_1ALAALAASPASPBA512 - 6641 - 153
d_22ens_1NAGNAGNAGNAGMM1
d_23ens_1NAGNAGNAGNAGMM2
d_24ens_1NAGNAGNAGNAGBLB701
d_25ens_1NAGNAGNAGNAGNN1
d_26ens_1NAGNAGNAGNAGNN2
d_31ens_1ALAALAASPASPFE512 - 6641 - 153
d_32ens_1NAGNAGNAGNAGuUA1
d_33ens_1NAGNAGNAGNAGuUA2
d_34ens_1NAGNAGNAGNAGFTB701
d_35ens_1NAGNAGNAGNAGvVA1
d_36ens_1NAGNAGNAGNAGvVA2
d_11ens_2GLUGLUVALVALCD32 - 5052 - 473
d_12ens_2NAGNAGNAGNAGfFA1
d_13ens_2NAGNAGNAGNAGfFA2
d_14ens_2BMABMABMABMAfFA3
d_15ens_2MANMANMANMANfFA4
d_16ens_2MANMANMANMANfFA5
d_17ens_2NAGNAGNAGNAGgGA1
d_18ens_2NAGNAGNAGNAGgGA2
d_19ens_2NAGNAGNAGNAGCQB601
d_110ens_2NAGNAGNAGNAGhHA1
d_111ens_2NAGNAGNAGNAGhHA2
d_112ens_2BMABMABMABMAhHA3
d_113ens_2NAGNAGNAGNAGiIA1
d_114ens_2NAGNAGNAGNAGiIA2
d_115ens_2NAGNAGNAGNAGjJA1
d_116ens_2NAGNAGNAGNAGjJA2
d_117ens_2NAGNAGNAGNAGkKA1
d_118ens_2NAGNAGNAGNAGkKA2
d_119ens_2NAGNAGNAGNAGlLA1
d_120ens_2NAGNAGNAGNAGlLA2
d_121ens_2BMABMABMABMAlLA3
d_122ens_2MANMANMANMANlLA4
d_123ens_2MANMANMANMANlLA5
d_124ens_2MANMANMANMANlLA6
d_125ens_2NAGNAGNAGNAGmMA1
d_126ens_2NAGNAGNAGNAGmMA2
d_127ens_2BMABMABMABMAmMA3
d_128ens_2MANMANMANMANmMA4
d_129ens_2MANMANMANMANmMA5
d_130ens_2NAGNAGNAGNAGnNA1
d_131ens_2NAGNAGNAGNAGnNA2
d_132ens_2NAGNAGNAGNAGoOA1
d_133ens_2NAGNAGNAGNAGoOA2
d_134ens_2NAGNAGNAGNAGCRB602
d_135ens_2NAGNAGNAGNAGpPA1
d_136ens_2NAGNAGNAGNAGpPA2
d_137ens_2NAGNAGNAGNAGCSB603
d_138ens_2NAGNAGNAGNAGqQA1
d_139ens_2NAGNAGNAGNAGqQA2
d_140ens_2NAGNAGNAGNAGrRA1
d_141ens_2NAGNAGNAGNAGrRA2
d_142ens_2BMABMABMABMArRA3
d_143ens_2NAGNAGNAGNAGsSA1
d_144ens_2NAGNAGNAGNAGsSA2
d_145ens_2NAGNAGNAGNAGtTA1
d_146ens_2NAGNAGNAGNAGtTA2
d_147ens_2BMABMABMABMAtTA3
d_148ens_2MANMANMANMANtTA4
d_149ens_2MANMANMANMANtTA5
d_21ens_2GLUGLUVALVALGB32 - 5052 - 473
d_22ens_2NAGNAGNAGNAGOO1
d_23ens_2NAGNAGNAGNAGOO2
d_24ens_2BMABMABMABMAOO3
d_25ens_2MANMANMANMANOO4
d_26ens_2MANMANMANMANOO5
d_27ens_2NAGNAGNAGNAGPP1
d_28ens_2NAGNAGNAGNAGPP2
d_29ens_2NAGNAGNAGNAGGMB601
d_210ens_2NAGNAGNAGNAGQQ1
d_211ens_2NAGNAGNAGNAGQQ2
d_212ens_2BMABMABMABMAQQ3
d_213ens_2NAGNAGNAGNAGRR1
d_214ens_2NAGNAGNAGNAGRR2
d_215ens_2NAGNAGNAGNAGSS1
d_216ens_2NAGNAGNAGNAGSS2
d_217ens_2NAGNAGNAGNAGTT1
d_218ens_2NAGNAGNAGNAGTT2
d_219ens_2NAGNAGNAGNAGUU1
d_220ens_2NAGNAGNAGNAGUU2
d_221ens_2BMABMABMABMAUU3
d_222ens_2MANMANMANMANUU4
d_223ens_2MANMANMANMANUU5
d_224ens_2MANMANMANMANUU6
d_225ens_2NAGNAGNAGNAGVV1
d_226ens_2NAGNAGNAGNAGVV2
d_227ens_2BMABMABMABMAVV3
d_228ens_2MANMANMANMANVV4
d_229ens_2MANMANMANMANVV5
d_230ens_2NAGNAGNAGNAGWW1
d_231ens_2NAGNAGNAGNAGWW2
d_232ens_2NAGNAGNAGNAGXX1
d_233ens_2NAGNAGNAGNAGXX2
d_234ens_2NAGNAGNAGNAGGNB602
d_235ens_2NAGNAGNAGNAGYY1
d_236ens_2NAGNAGNAGNAGYY2
d_237ens_2NAGNAGNAGNAGGOB603
d_238ens_2NAGNAGNAGNAGZZ1
d_239ens_2NAGNAGNAGNAGZZ2
d_240ens_2NAGNAGNAGNAGaAA1
d_241ens_2NAGNAGNAGNAGaAA2
d_242ens_2BMABMABMABMAaAA3
d_243ens_2NAGNAGNAGNAGbBA1
d_244ens_2NAGNAGNAGNAGbBA2
d_245ens_2NAGNAGNAGNAGcCA1
d_246ens_2NAGNAGNAGNAGcCA2
d_247ens_2BMABMABMABMAcCA3
d_248ens_2MANMANMANMANcCA4
d_249ens_2MANMANMANMANcCA5
d_31ens_2GLUGLUVALVALIF32 - 5052 - 473
d_32ens_2NAGNAGNAGNAGwWA1
d_33ens_2NAGNAGNAGNAGwWA2
d_34ens_2BMABMABMABMAwWA3
d_35ens_2MANMANMANMANwWA4
d_36ens_2MANMANMANMANwWA5
d_37ens_2NAGNAGNAGNAGxXA1
d_38ens_2NAGNAGNAGNAGxXA2
d_39ens_2NAGNAGNAGNAGIUB601
d_310ens_2NAGNAGNAGNAGyYA1
d_311ens_2NAGNAGNAGNAGyYA2
d_312ens_2BMABMABMABMAyYA3
d_313ens_2NAGNAGNAGNAGzZA1
d_314ens_2NAGNAGNAGNAGzZA2
d_315ens_2NAGNAGNAGNAG0AB1
d_316ens_2NAGNAGNAGNAG0AB2
d_317ens_2NAGNAGNAGNAG1BB1
d_318ens_2NAGNAGNAGNAG1BB2
d_319ens_2NAGNAGNAGNAG2CB1
d_320ens_2NAGNAGNAGNAG2CB2
d_321ens_2BMABMABMABMA2CB3
d_322ens_2MANMANMANMAN2CB4
d_323ens_2MANMANMANMAN2CB5
d_324ens_2MANMANMANMAN2CB6
d_325ens_2NAGNAGNAGNAG3DB1
d_326ens_2NAGNAGNAGNAG3DB2
d_327ens_2BMABMABMABMA3DB3
d_328ens_2MANMANMANMAN3DB4
d_329ens_2MANMANMANMAN3DB5
d_330ens_2NAGNAGNAGNAG4EB1
d_331ens_2NAGNAGNAGNAG4EB2
d_332ens_2NAGNAGNAGNAG5FB1
d_333ens_2NAGNAGNAGNAG5FB2
d_334ens_2NAGNAGNAGNAGIVB602
d_335ens_2NAGNAGNAGNAG6GB1
d_336ens_2NAGNAGNAGNAG6GB2
d_337ens_2NAGNAGNAGNAGIWB603
d_338ens_2NAGNAGNAGNAG7HB1
d_339ens_2NAGNAGNAGNAG7HB2
d_340ens_2NAGNAGNAGNAG8IB1
d_341ens_2NAGNAGNAGNAG8IB2
d_342ens_2BMABMABMABMA8IB3
d_343ens_2NAGNAGNAGNAG9JB1
d_344ens_2NAGNAGNAGNAG9JB2
d_345ens_2NAGNAGNAGNAGAAKB1
d_346ens_2NAGNAGNAGNAGAAKB2
d_347ens_2BMABMABMABMAAAKB3
d_348ens_2MANMANMANMANAAKB4
d_349ens_2MANMANMANMANAAKB5
d_11ens_3GLNGLNSERSERDI1 - 1131 - 132
d_21ens_3GLNGLNSERSERHG1 - 1131 - 132
d_31ens_3GLNGLNSERSERJK1 - 1131 - 132
d_11ens_4ALAALAARGARGEJ1 - 1081 - 108
d_21ens_4ALAALAARGARGKL1 - 1081 - 108
d_31ens_4ALAALAARGARGLH1 - 1081 - 108

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(-0.500190703134, 0.865915179038, -0.000403991445793), (-0.865915268506, -0.500190596954, 0.000338359705824), (9.09180828123E-5, 0.000519066740427, 0.999999861152)117.992018968, 439.857099039, -0.132085874713
2given(-0.49913683729, -0.866523161424, -0.000168452622938), (0.866523151319, -0.499136860665, 0.000150181761171), (-0.000214216887862, -7.10068483861E-5, 0.999999974535)439.849235234, 117.579540016, 0.0525306418654
3given(-0.500070165842, 0.865984876705, 0.000150177560123), (-0.865984883724, -0.500070175275, 3.1024707948E-5), (0.0001019662467, -0.000114536966092, 0.999999988242)117.864750368, 439.888691989, 0.00228718124333
4given(-0.499552923822, -0.866283361368, -0.00011881678283), (0.866283357005, -0.499552935219, 0.000101437549252), (-0.000147228933751, -5.22555771847E-5, 0.999999987796)439.875879313, 117.70480289, 0.0381417649872
5given(-0.502269631742, 0.864711049478, -0.000133940539023), (-0.86471093563, -0.502269470535, 0.000613816180445), (0.000463499389961, 0.000424121075726, 0.999999802645)118.63822372, 440.040730191, -0.200954113977
6given(-0.504479744943, -0.863422628178, 0.00124582994623), (0.863422550536, -0.504480819287, -0.000776014286107), (0.00129852560638, 0.000684194180583, 0.999998922854)440.054546224, 119.47921291, -0.434604302531
7given(-0.500419264735, -0.865782029269, -0.0014273321195), (0.865699714614, -0.500393221937, 0.01306244831), (-0.0120234603231, 0.00530105977042, 0.999913663857)440.072221179, 116.220462156, 1.43448233444
8given(-0.499411476495, 0.86617856846, -0.0179684358116), (-0.866353417717, -0.499404303402, 0.00520551185994), (-0.00446461135876, 0.0181667081403, 0.999825003669)120.374141469, 438.993940309, -3.13066911271

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Components

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

#1: Protein Envelope glycoprotein gp41 / Env polyprotein


Mass: 17134.404 Da / Num. of mol.: 3
Mutation: A517E, M535N, N543Q, T569G, I573F, R588E, D589V, S636G, N651F, K655I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: BG505 / Gene: env / Cell line (production host): 293Freestyle / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#2: Protein Envelope glycoprotein gp120


Mass: 53262.453 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: BG505 / Gene: env / Cell line (production host): 293Freestyle / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6

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Antibody , 2 types, 6 molecules HDJLEK

#3: Antibody antibody ACS202 Fab heavy chain


Mass: 25295.486 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi293 / Production host: Homo sapiens (human)
#4: Antibody antibody ACS202 Fab light chain


Mass: 23470.197 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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.: 33 / Source method: obtained synthetically
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
#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.: 9 / Source method: isolated from a natural 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
#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.: 6
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
#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-ROHGlycam 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
[][D-1-deoxy-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.: 12 / 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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Non-polymers , 1 types, 369 molecules

#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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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
IDNameTypeDetailsEntity IDParent-IDSource
1HIV-1 Env trimer complexed with antibody FabCOMPLEXgp41 and gp120 expressed as a single polypeptide, post translationally cleaved; antibody expressed and purified separately; purified Env trimer and Fab were mixed to make complex#1-#40RECOMBINANT
2antibody FabCOMPLEX#3-#41RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Human immunodeficiency virus 111676BG505
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606293Freestyle
32Homo sapiens (human)9606expi293
Buffer solutionpH: 7.4 / Details: PBS with 0.1 mM DTT
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / 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: 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 (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3particle selection
4cryoSPARC3.3CTF correction
7UCSF Chimeramodel fitting
9UCSF Chimera1.16initial Euler assignment
12cryoSPARC3.33D reconstruction
13PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 635332 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 86.91 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003322059
ELECTRON MICROSCOPYf_angle_d0.503229907
ELECTRON MICROSCOPYf_chiral_restr0.04363798
ELECTRON MICROSCOPYf_plane_restr0.0043585
ELECTRON MICROSCOPYf_dihedral_angle_d15.68218391
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CAELECTRON MICROSCOPYNCS constraints0.000700868438555
ens_1d_3CAELECTRON MICROSCOPYNCS constraints0.000715700220235
ens_2d_2DCELECTRON MICROSCOPYNCS constraints0.0626660732699
ens_2d_3DCELECTRON MICROSCOPYNCS constraints0.000706034629692
ens_3d_2IDELECTRON MICROSCOPYNCS constraints0.000711946778804
ens_3d_3IDELECTRON MICROSCOPYNCS constraints0.000709100761443
ens_4d_2JEELECTRON MICROSCOPYNCS constraints0.00069947123962
ens_4d_3JEELECTRON MICROSCOPYNCS constraints0.000700281649132

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