[English] 日本語
Yorodumi
- PDB-5feh: Crystal structure of PCT64_35B, a broadly neutralizing anti-HIV a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5feh
TitleCrystal structure of PCT64_35B, a broadly neutralizing anti-HIV antibody
Components
  • PCT64_26 Fab heavy chain
  • PCT64_26 Fab light chain
KeywordsIMMUNE SYSTEM / HIV / broadly neutralizing antibody / V1/V2
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMurrell, S. / Wilson, I.A.
CitationJournal: Immunity / Year: 2017
Title: HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage.
Authors: Elise Landais / Ben Murrell / Bryan Briney / Sasha Murrell / Kimmo Rantalainen / Zachary T Berndsen / Alejandra Ramos / Lalinda Wickramasinghe / Melissa Laird Smith / Kemal Eren / Natalia de ...Authors: Elise Landais / Ben Murrell / Bryan Briney / Sasha Murrell / Kimmo Rantalainen / Zachary T Berndsen / Alejandra Ramos / Lalinda Wickramasinghe / Melissa Laird Smith / Kemal Eren / Natalia de Val / Mengyu Wu / Audrey Cappelletti / Jeffrey Umotoy / Yolanda Lie / Terri Wrin / Paul Algate / Po-Ying Chan-Hui / Etienne Karita / / / Andrew B Ward / Ian A Wilson / Dennis R Burton / Davey Smith / Sergei L Kosakovsky Pond / Pascal Poignard /
Abstract: Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb ...Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb lineage targeting the Env V2 apex and the Ab-Env co-evolution that led to development of neutralization breadth. The lineage Abs bore an anionic heavy chain complementarity-determining region 3 (CDRH3) of 25 amino acids, among the shortest known for this class of Abs, and achieved breadth with only 10% nucleotide somatic hypermutation and no insertions or deletions. The data suggested a role for Env glycoform heterogeneity in the activation of the lineage germline B cell. Finally, we showed that localized diversity at key V2 epitope residues drove bnAb maturation toward breadth, mirroring the Env evolution pattern described for another donor who developed V2-apex targeting bnAbs. Overall, these findings suggest potential strategies for vaccine approaches based on germline-targeting and serial immunogen design.
History
DepositionDec 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PCT64_26 Fab light chain
B: PCT64_26 Fab heavy chain
C: PCT64_26 Fab light chain
D: PCT64_26 Fab heavy chain
E: PCT64_26 Fab light chain
F: PCT64_26 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,0048
Polymers149,8466
Non-polymers1582
Water543
1
A: PCT64_26 Fab light chain
B: PCT64_26 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0453
Polymers49,9492
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-32 kcal/mol
Surface area19490 Å2
MethodPISA
2
C: PCT64_26 Fab light chain
D: PCT64_26 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)49,9492
Polymers49,9492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-23 kcal/mol
Surface area20210 Å2
MethodPISA
3
E: PCT64_26 Fab light chain
F: PCT64_26 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0113
Polymers49,9492
Non-polymers621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-24 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.525, 135.525, 353.602
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Antibody PCT64_26 Fab light chain


Mass: 23549.037 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody PCT64_26 Fab heavy chain


Mass: 26399.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: ammonium sulfate, ethylene glycol, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.1→48.892 Å / Num. obs: 35800 / % possible obs: 99.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.8
Reflection shellResolution: 3.1→3.17 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.9 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DFB

1dfb


Resolution: 3.1→48.892 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 1810 5.07 %
Rwork0.2592 --
obs0.2602 35719 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9667 0 9 3 9679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049902
X-RAY DIFFRACTIONf_angle_d0.76513453
X-RAY DIFFRACTIONf_dihedral_angle_d14.4233604
X-RAY DIFFRACTIONf_chiral_restr0.0471503
X-RAY DIFFRACTIONf_plane_restr0.0051721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.17970.36641280.34642527X-RAY DIFFRACTION99
3.1797-3.27330.34721720.33792521X-RAY DIFFRACTION100
3.2733-3.37890.3471550.31642548X-RAY DIFFRACTION100
3.3789-3.49960.29261200.29412580X-RAY DIFFRACTION100
3.4996-3.63970.30561430.28122524X-RAY DIFFRACTION98
3.6397-3.80530.2791110.28022613X-RAY DIFFRACTION100
3.8053-4.00580.24991450.27242584X-RAY DIFFRACTION100
4.0058-4.25670.31741480.25132593X-RAY DIFFRACTION100
4.2567-4.58510.24131410.21532591X-RAY DIFFRACTION100
4.5851-5.04610.26071310.21162607X-RAY DIFFRACTION99
5.0461-5.77530.24581420.22982639X-RAY DIFFRACTION100
5.7753-7.27240.26191390.26282682X-RAY DIFFRACTION99
7.2724-48.89780.24391350.23572900X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.38160.1097-0.04830.2164-0.00620.3422-0.05540.1393-0.0663-0.2044-0.0787-0.08130.12690.19060.07770.60630.2465-0.12290.4585-0.00150.5511-36.3504-53.8113-33.0476
20.2607-0.06370.02760.25820.05890.52840.1279-0.0219-0.44880.08460.12910.15160.49460.0974-0.19750.8420.2197-0.1780.3727-0.0790.71-37.7663-65.206-33.4253
30.95380.1414-0.64920.0258-0.05851.03330.07450.3484-0.0543-0.0979-0.02550.04670.10160.12650.00090.69920.3026-0.2310.4031-0.10980.4954-40.2439-60.7036-39.0942
40.46430.29930.15010.3547-0.2240.58020.09820.3155-0.3519-0.2320.130.23170.50330.1357-0.13350.75760.4802-0.07190.48560.03380.3905-35.5842-61.8146-31.0442
51.4206-1.61850.27274.2566-0.06381.2657-0.0597-0.00210.02540.23040.1142-0.09540.01310.0685-0.01940.61960.2692-0.01610.29790.0530.3284-39.5214-44.215-20.5066
66.45991.41621.56923.49690.87436.40040.18970.23040.41590.5334-0.1455-0.77280.01080.8693-0.03050.33430.1785-0.07950.36740.03690.6921-21.7973-39.2574-9.5097
77.35456.45530.31496.22271.97785.2019-0.11890.54891.3726-0.18230.3214-0.6188-0.25230.879-0.27150.44370.1240.18490.72290.17871.0493-15.3893-37.1634-16.2757
81.92081.54191.43535.923-0.45555.0810.02380.64960.4020.33880.0085-0.9646-0.25970.9473-0.04680.39970.16290.00780.38490.04320.6852-21.6249-39.2575-11.549
92.00470.02357.35668.51160.94886.7849-0.8501-0.05532.20820.2760.2039-0.9567-1.0660.43130.77330.41030.10060.10840.61950.11240.8837-23.9893-29.2335-11.0462
108.36271.63522.70411.1937-0.57282.50520.2705-0.1473-1.8165-0.8024-0.00060.01791.1969-0.0639-0.32721.13020.5933-0.12250.80940.10920.7479-22.5719-73.6017-20.0204
111.3317-0.61340.16410.3319-0.23960.76890.01470.3078-1.365-0.7562-0.22810.61741.13350.1469-0.23251.05781.8006-0.8070.01740.77850.3378-19.6747-72.6633-22.642
126.98783.7482-3.27485.3371.43454.60220.12671.16831.365-0.8272-0.40770.9228-0.8407-0.55290.2380.87370.1415-0.21240.84890.20230.5129-25.7734-38.2408-0.1896
133.015-0.55040.36413.6925-1.17231.507-0.0973-0.43190.33170.99320.0692-0.1506-0.16140.44750.02010.51530.4204-0.04870.49350.03850.3861-24.3532-50.1022-0.487
140.5870.11740.14340.6448-0.2670.19450.2386-0.0291-0.0197-0.0230.23180.96450.1202-0.692-0.23640.6283-0.3064-0.1580.99940.24710.8979-20.8102-103.879715.6973
151.11410.14960.01160.74430.05760.70580.026-0.0312-0.1759-0.14110.24530.76880.518-0.6956-0.14070.4062-0.1424-0.20330.56640.23130.7121-13.8317-100.468213.1903
161.63580.03210.07934.96150.33182.6805-0.11380.23080.51340.03440.15540.0812-0.39140.0067-0.04360.22890.0656-0.07920.16850.09860.33547.9259-80.79910.8916
175.56593.81320.2915.01222.88976.59960.6139-0.54970.59221.22630.0922-0.2989-0.49910.336-0.56990.8372-0.0735-0.11940.26010.07490.56166.3064-77.357420.1533
183.63081.82780.45776.98040.58083.1634-0.04450.50560.3177-0.05930.1096-0.0556-0.12240.2216-0.08120.1987-0.0101-0.08050.20360.05580.25669.9674-82.127513.4948
190.54920.1035-0.25050.382-0.28180.22320.2754-0.1067-0.1233-0.27040.13691.03150.3396-0.8337-0.22220.65410.2044-0.12891.18990.31851.3996-31.6114-83.49948.8373
201.3197-0.2692-0.162.648-0.33511.8750.06480.0809-0.3615-0.4581-0.1488-0.0795-0.1174-0.1780.03550.47580.2104-0.03740.40610.08370.3371-2.9968-78.5860.8655
210.31820.0548-0.03570.2958-0.06430.17180.1475-0.156-0.20590.203-0.19780.1320.40060.28250.04350.23610.33260.01130.4865-0.01680.2687-29.0712-42.7251-39.9565
220.0565-0.06910.04930.1739-0.01520.19380.05580.11960.0396-0.1977-0.1535-0.05350.11390.27320.0363-0.00330.4986-0.21190.7061-0.08810.3329-26.6937-39.4003-52.1328
230.1201-0.0388-0.10930.06660.08390.15980.07690.0049-0.10260.06720.05460.18020.1287-0.0057-0.03660.3530.1968-0.0450.3097-0.06790.3457-33.3661-45.6297-43.2713
240.6028-0.2375-0.18980.2177-0.07120.3021-0.05930.3723-0.27420.0168-0.230.27540.27170.20310.10940.24250.2097-0.02370.4118-0.04790.3049-25.8163-40.1627-43.9657
252.5814-0.80850.51091.0373-0.3471.2956-0.1891-0.85930.38980.4243-0.2965-0.4684-0.22191.14860.2414-0.04270.86770.08081.66360.07270.44093.016-43.3627-31.0954
261.97330.0911-0.80691.7496-0.43480.5002-0.1887-1.020.29920.5229-0.0837-0.1333-0.01970.65850.17810.55390.4489-0.1021.3250.21160.2429-5.4106-47.9417-29.0352
272.66451.0288-0.32982.7383-0.03230.05150.4001-1.32570.05891.2594-0.3498-0.57860.02780.56760.03620.20050.7107-0.19741.96870.15570.51861.818-44.0381-24.6034
280.8680.2668-0.56331.39750.43561.3567-0.03260.24160.4604-0.7218-0.10.0476-0.44430.30990.10550.52660.0222-0.00860.42520.04730.541-24.8716-18.9727-45.8151
290.3868-0.2081-0.82071.61840.2691.39690.01510.18260.64120.0617-0.0504-0.6021-0.47350.99490.0204-0.02750.05930.15051.25750.01490.6315-4.6614-32.4498-43.5852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:18 )A1 - 18
2X-RAY DIFFRACTION2( CHAIN A AND RESID 19:61 )A19 - 61
3X-RAY DIFFRACTION3( CHAIN A AND RESID 62:75 )A62 - 75
4X-RAY DIFFRACTION4( CHAIN A AND RESID 76:102 )A76 - 102
5X-RAY DIFFRACTION5( CHAIN A AND RESID 103:114 )A103 - 114
6X-RAY DIFFRACTION6( CHAIN A AND RESID 115:150 )A115 - 150
7X-RAY DIFFRACTION7( CHAIN A AND RESID 151:164 )A151 - 164
8X-RAY DIFFRACTION8( CHAIN A AND RESID 165:199 )A165 - 199
9X-RAY DIFFRACTION9( CHAIN A AND RESID 200:214 )A200 - 214
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1:44 )B1 - 44
11X-RAY DIFFRACTION11( CHAIN B AND RESID 45:120 )B45 - 120
12X-RAY DIFFRACTION12( CHAIN B AND RESID 121:136 )B121 - 136
13X-RAY DIFFRACTION13( CHAIN B AND RESID 137:215 )B137 - 215
14X-RAY DIFFRACTION14( CHAIN C AND RESID 1:75 )C1 - 75
15X-RAY DIFFRACTION15( CHAIN C AND RESID 76:114 )C76 - 114
16X-RAY DIFFRACTION16( CHAIN C AND RESID 115:150 )C115 - 150
17X-RAY DIFFRACTION17( CHAIN C AND RESID 151:164 )C151 - 164
18X-RAY DIFFRACTION18( CHAIN C AND RESID 165:215 )C165 - 215
19X-RAY DIFFRACTION19( CHAIN D AND RESID 2:82 )D2 - 82
20X-RAY DIFFRACTION20( CHAIN D AND RESID 83:217 )D83 - 217
21X-RAY DIFFRACTION21( CHAIN E AND RESID 1:38 )E1 - 38
22X-RAY DIFFRACTION22( CHAIN E AND RESID 39:61 )E39 - 61
23X-RAY DIFFRACTION23( CHAIN E AND RESID 62:75 )E62 - 75
24X-RAY DIFFRACTION24( CHAIN E AND RESID 76:102 )E76 - 102
25X-RAY DIFFRACTION25( CHAIN E AND RESID 103:138 )E103 - 138
26X-RAY DIFFRACTION26( CHAIN E AND RESID 139:150 )E139 - 150
27X-RAY DIFFRACTION27( CHAIN E AND RESID 151:214 )E151 - 214
28X-RAY DIFFRACTION28( CHAIN F AND RESID 1:82 )F1 - 82
29X-RAY DIFFRACTION29( CHAIN F AND RESID 83:214 )F83 - 214

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more