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- PDB-9pq2: Cryo-EM structure of HIV-1 459C-WT DS-SOSIP RnS Env trimer -

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Basic information

Entry
Database: PDB / ID: 9pq2
TitleCryo-EM structure of HIV-1 459C-WT DS-SOSIP RnS Env trimer
Components(459C-WT RnS DS-SOSIP ...) x 2
KeywordsVIRAL PROTEIN / Envelope trimer / 459C-WT / RnS DS-SOSIP immunogen
Biological speciesHuman immunodeficiency virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 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 22, 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
C: 459C-WT RnS DS-SOSIP gp120
A: 459C-WT RnS DS-SOSIP gp41
G: 459C-WT RnS DS-SOSIP gp120
B: 459C-WT RnS DS-SOSIP gp41
I: 459C-WT RnS DS-SOSIP gp120
F: 459C-WT RnS DS-SOSIP gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,40466
Polymers216,0406
Non-polymers33,36460
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 "A"
d_2ens_1chain "B"
d_3ens_1chain "F"
d_1ens_2chain "C"
d_2ens_2chain "G"
d_3ens_2chain "I"

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_1LEULEUASPASPAB520 - 6649 - 153
d_21ens_1LEULEUASPASPBD520 - 6649 - 153
d_31ens_1LEULEUASPASPFF520 - 6649 - 153
d_11ens_2GLYGLYVALVALCA32 - 5051 - 484
d_12ens_2NAGNAGNAGNAGCFB601
d_13ens_2NAGNAGNAGNAGDG1
d_14ens_2NAGNAGNAGNAGDG2
d_15ens_2NAGNAGNAGNAGEH1
d_16ens_2NAGNAGNAGNAGEH2
d_17ens_2BMABMABMABMAEH3
d_18ens_2MANMANMANMANEH4
d_19ens_2MANMANMANMANEH5
d_110ens_2NAGNAGNAGNAGHI1
d_111ens_2NAGNAGNAGNAGHI2
d_112ens_2BMABMABMABMAHI3
d_113ens_2NAGNAGNAGNAGJJ1
d_114ens_2NAGNAGNAGNAGJJ2
d_115ens_2BMABMABMABMAJJ3
d_116ens_2NAGNAGNAGNAGKK1
d_117ens_2NAGNAGNAGNAGKK2
d_118ens_2BMABMABMABMAKK3
d_119ens_2NAGNAGNAGNAGLL1
d_120ens_2NAGNAGNAGNAGLL2
d_121ens_2BMABMABMABMALL3
d_122ens_2MANMANMANMANLL4
d_123ens_2MANMANMANMANLL5
d_124ens_2MANMANMANMANLL6
d_125ens_2NAGNAGNAGNAGMM1
d_126ens_2NAGNAGNAGNAGMM2
d_127ens_2BMABMABMABMAMM3
d_128ens_2NAGNAGNAGNAGNN1
d_129ens_2NAGNAGNAGNAGNN2
d_130ens_2BMABMABMABMANN3
d_131ens_2MANMANMANMANNN4
d_132ens_2NAGNAGNAGNAGOO1
d_133ens_2NAGNAGNAGNAGOO2
d_134ens_2NAGNAGNAGNAGPP1
d_135ens_2NAGNAGNAGNAGPP2
d_136ens_2BMABMABMABMAPP3
d_137ens_2NAGNAGNAGNAGQQ1
d_138ens_2NAGNAGNAGNAGQQ2
d_139ens_2BMABMABMABMAQQ3
d_140ens_2MANMANMANMANQQ4
d_141ens_2MANMANMANMANQQ5
d_142ens_2NAGNAGNAGNAGRR1
d_143ens_2NAGNAGNAGNAGRR2
d_144ens_2BMABMABMABMARR3
d_145ens_2NAGNAGNAGNAGSS1
d_146ens_2NAGNAGNAGNAGSS2
d_147ens_2NAGNAGNAGNAGTT1
d_148ens_2NAGNAGNAGNAGTT2
d_149ens_2BMABMABMABMATT3
d_150ens_2NAGNAGNAGNAGUU1
d_151ens_2NAGNAGNAGNAGUU2
d_152ens_2BMABMABMABMAUU3
d_153ens_2NAGNAGNAGNAGCGB602
d_154ens_2NAGNAGNAGNAGCHB603
d_155ens_2NAGNAGNAGNAGVV1
d_156ens_2NAGNAGNAGNAGVV2
d_157ens_2NAGNAGNAGNAGWW1
d_158ens_2NAGNAGNAGNAGWW2
d_21ens_2GLYGLYVALVALGC32 - 5051 - 484
d_22ens_2NAGNAGNAGNAGGIB601
d_23ens_2NAGNAGNAGNAGXX1
d_24ens_2NAGNAGNAGNAGXX2
d_25ens_2NAGNAGNAGNAGYY1
d_26ens_2NAGNAGNAGNAGYY2
d_27ens_2BMABMABMABMAYY3
d_28ens_2MANMANMANMANYY4
d_29ens_2MANMANMANMANYY5
d_210ens_2NAGNAGNAGNAGZZ1
d_211ens_2NAGNAGNAGNAGZZ2
d_212ens_2BMABMABMABMAZZ3
d_213ens_2NAGNAGNAGNAGaAA1
d_214ens_2NAGNAGNAGNAGaAA2
d_215ens_2BMABMABMABMAaAA3
d_216ens_2NAGNAGNAGNAGbBA1
d_217ens_2NAGNAGNAGNAGbBA2
d_218ens_2BMABMABMABMAbBA3
d_219ens_2NAGNAGNAGNAGcCA1
d_220ens_2NAGNAGNAGNAGcCA2
d_221ens_2BMABMABMABMAcCA3
d_222ens_2MANMANMANMANcCA4
d_223ens_2MANMANMANMANcCA5
d_224ens_2MANMANMANMANcCA6
d_225ens_2NAGNAGNAGNAGdDA1
d_226ens_2NAGNAGNAGNAGdDA2
d_227ens_2BMABMABMABMAdDA3
d_228ens_2NAGNAGNAGNAGeEA1
d_229ens_2NAGNAGNAGNAGeEA2
d_230ens_2BMABMABMABMAeEA3
d_231ens_2MANMANMANMANeEA4
d_232ens_2NAGNAGNAGNAGfFA1
d_233ens_2NAGNAGNAGNAGfFA2
d_234ens_2NAGNAGNAGNAGgGA1
d_235ens_2NAGNAGNAGNAGgGA2
d_236ens_2BMABMABMABMAgGA3
d_237ens_2NAGNAGNAGNAGhHA1
d_238ens_2NAGNAGNAGNAGhHA2
d_239ens_2BMABMABMABMAhHA3
d_240ens_2MANMANMANMANhHA4
d_241ens_2MANMANMANMANhHA5
d_242ens_2NAGNAGNAGNAGiIA1
d_243ens_2NAGNAGNAGNAGiIA2
d_244ens_2BMABMABMABMAiIA3
d_245ens_2NAGNAGNAGNAGjJA1
d_246ens_2NAGNAGNAGNAGjJA2
d_247ens_2NAGNAGNAGNAGkKA1
d_248ens_2NAGNAGNAGNAGkKA2
d_249ens_2BMABMABMABMAkKA3
d_250ens_2NAGNAGNAGNAGlLA1
d_251ens_2NAGNAGNAGNAGlLA2
d_252ens_2BMABMABMABMAlLA3
d_253ens_2NAGNAGNAGNAGGJB602
d_254ens_2NAGNAGNAGNAGGKB603
d_255ens_2NAGNAGNAGNAGmMA1
d_256ens_2NAGNAGNAGNAGmMA2
d_257ens_2NAGNAGNAGNAGnNA1
d_258ens_2NAGNAGNAGNAGnNA2
d_31ens_2GLYGLYVALVALIE32 - 5051 - 484
d_32ens_2NAGNAGNAGNAGILB601
d_33ens_2NAGNAGNAGNAGoOA1
d_34ens_2NAGNAGNAGNAGoOA2
d_35ens_2NAGNAGNAGNAGpPA1
d_36ens_2NAGNAGNAGNAGpPA2
d_37ens_2BMABMABMABMApPA3
d_38ens_2MANMANMANMANpPA4
d_39ens_2MANMANMANMANpPA5
d_310ens_2NAGNAGNAGNAGqQA1
d_311ens_2NAGNAGNAGNAGqQA2
d_312ens_2BMABMABMABMAqQA3
d_313ens_2NAGNAGNAGNAGrRA1
d_314ens_2NAGNAGNAGNAGrRA2
d_315ens_2BMABMABMABMArRA3
d_316ens_2NAGNAGNAGNAGsSA1
d_317ens_2NAGNAGNAGNAGsSA2
d_318ens_2BMABMABMABMAsSA3
d_319ens_2NAGNAGNAGNAGtTA1
d_320ens_2NAGNAGNAGNAGtTA2
d_321ens_2BMABMABMABMAtTA3
d_322ens_2MANMANMANMANtTA4
d_323ens_2MANMANMANMANtTA5
d_324ens_2MANMANMANMANtTA6
d_325ens_2NAGNAGNAGNAGuUA1
d_326ens_2NAGNAGNAGNAGuUA2
d_327ens_2BMABMABMABMAuUA3
d_328ens_2NAGNAGNAGNAGvVA1
d_329ens_2NAGNAGNAGNAGvVA2
d_330ens_2BMABMABMABMAvVA3
d_331ens_2MANMANMANMANvVA4
d_332ens_2NAGNAGNAGNAGwWA1
d_333ens_2NAGNAGNAGNAGwWA2
d_334ens_2NAGNAGNAGNAGxXA1
d_335ens_2NAGNAGNAGNAGxXA2
d_336ens_2BMABMABMABMAxXA3
d_337ens_2NAGNAGNAGNAGyYA1
d_338ens_2NAGNAGNAGNAGyYA2
d_339ens_2BMABMABMABMAyYA3
d_340ens_2MANMANMANMANyYA4
d_341ens_2MANMANMANMANyYA5
d_342ens_2NAGNAGNAGNAGzZA1
d_343ens_2NAGNAGNAGNAGzZA2
d_344ens_2BMABMABMABMAzZA3
d_345ens_2NAGNAGNAGNAG0AB1
d_346ens_2NAGNAGNAGNAG0AB2
d_347ens_2NAGNAGNAGNAG1BB1
d_348ens_2NAGNAGNAGNAG1BB2
d_349ens_2BMABMABMABMA1BB3
d_350ens_2NAGNAGNAGNAG2CB1
d_351ens_2NAGNAGNAGNAG2CB2
d_352ens_2BMABMABMABMA2CB3
d_353ens_2NAGNAGNAGNAGIMB602
d_354ens_2NAGNAGNAGNAGINB603
d_355ens_2NAGNAGNAGNAG3DB1
d_356ens_2NAGNAGNAGNAG3DB2
d_357ens_2NAGNAGNAGNAG4EB1
d_358ens_2NAGNAGNAGNAG4EB2

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.491365862733, -0.870952083206, 0.0014344682654), (0.870951245614, -0.491360511042, 0.00296242340938), (-0.00187528777977, 0.00270498565688, 0.999994583159)420.621973797, 110.048074539, -0.164618555292
2given(-0.501097573702, 0.865383440249, -0.00356692769275), (-0.86538825955, -0.501101821274, -0.000353480073144), (-0.00209328976495, 0.00290964934097, 0.999993576019)113.818413708, 421.683559666, -0.269842341428
3given(-0.502616811431, -0.86449661435, 0.00468451105789), (0.864495500303, -0.502632029557, -0.00292793770353), (0.00488577753223, 0.00257810801805, 0.999984741152)421.087627691, 114.312329566, -1.50488704613
4given(-0.502963137031, 0.864305712591, -0.0019282042203), (-0.864307827865, -0.502961224699, 0.0014089504276), (0.000247951947224, 0.00237521212832, 0.99999714844)114.295532566, 421.450253573, -0.490343501952

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Components

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459C-WT RnS DS-SOSIP ... , 2 types, 6 molecules CGIABF

#1: Protein 459C-WT RnS DS-SOSIP gp120


Mass: 54848.867 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK-Expi293 / Production host: Homo sapiens (human)
#2: Protein 459C-WT RnS DS-SOSIP gp41


Mass: 17164.449 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK-Expi293 / Production host: Homo sapiens (human)

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Sugars , 6 types, 60 molecules

#3: 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.: 15
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
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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.: 9 / 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 459C-WT RnS DS-SOSIP / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK-Expi293
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
1cryoSPARC4.4.1particle selection
4cryoSPARC4.4.1CTF correction
7UCSF ChimeraX1.9model fitting
9PHENIX1.21.2_5419model refinement
10UCSF ChimeraX1.9initial Euler assignment
12cryoSPARC4.4.1classification
13cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 207797 / 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: 90.35 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00416461
ELECTRON MICROSCOPYf_angle_d0.905822380
ELECTRON MICROSCOPYf_chiral_restr0.05163051
ELECTRON MICROSCOPYf_plane_restr0.00542595
ELECTRON MICROSCOPYf_dihedral_angle_d13.34698211
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BAELECTRON MICROSCOPYNCS constraints0.000705521100455
ens_1d_3BAELECTRON MICROSCOPYNCS constraints0.000710960344495
ens_2d_2ACELECTRON MICROSCOPYNCS constraints0.00070544314668
ens_2d_3ACELECTRON MICROSCOPYNCS constraints0.000699921422819

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