[English] 日本語
Yorodumi
- PDB-6ca9: Crystal structure of Fab PCT64_LMCA (SAR), the least mutated comm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ca9
TitleCrystal structure of Fab PCT64_LMCA (SAR), the least mutated common ancestor of the HIV-1 broadly neutralizing antibody lineage PCT64
Components
  • PCT64_LMCA Fab heavy chain
  • PCT64_LMCA Fab light chain
KeywordsIMMUNE SYSTEM / IgG1 / Antibody / HIV-1 / bNAb
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsOmorodion, O. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
International AIDS Vaccine InitiativeOPP1084519 United States
CitationJournal: Cell Rep / Year: 2018
Title: Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design.
Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais ...Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais / James C Paulson / Ian A Wilson / Andrew B Ward /
Abstract: Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at ...Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex.
History
DepositionJan 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PCT64_LMCA Fab light chain
B: PCT64_LMCA Fab heavy chain
C: PCT64_LMCA Fab light chain
D: PCT64_LMCA Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2216
Polymers98,0234
Non-polymers1982
Water57632
1
A: PCT64_LMCA Fab light chain
B: PCT64_LMCA Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2104
Polymers49,0112
Non-polymers1982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-19 kcal/mol
Surface area20430 Å2
MethodPISA
2
C: PCT64_LMCA Fab light chain
D: PCT64_LMCA Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)49,0112
Polymers49,0112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-21 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.199, 87.158, 142.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody PCT64_LMCA Fab light chain


Mass: 23273.805 Da / Num. of mol.: 2 / Mutation: Y91S, G92A, S93R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody PCT64_LMCA Fab heavy chain


Mass: 25737.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris (pH 8), 1 M lithium chloride, 10% w/v PEG 6000, cryoprotected with 30% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 27556 / % possible obs: 93.4 % / Redundancy: 5.9 % / Rsym value: 0.12 / Net I/σ(I): 12.4
Reflection shellResolution: 2.7→2.75 Å / Num. unique all: 998 / CC1/2: 0.91 / Rsym value: 0.47

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-20002.3.10data reduction
SCALEPACKdata scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FEH, 1NGZ

5feh

1ngz


Resolution: 2.702→43.579 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.27
RfactorNum. reflection% reflection
Rfree0.2683 1340 4.88 %
Rwork0.2415 --
obs0.2429 27451 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.702→43.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6769 0 10 32 6811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026947
X-RAY DIFFRACTIONf_angle_d0.4879454
X-RAY DIFFRACTIONf_dihedral_angle_d18.6632496
X-RAY DIFFRACTIONf_chiral_restr0.0421054
X-RAY DIFFRACTIONf_plane_restr0.0041200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7017-2.79830.38841020.36391905X-RAY DIFFRACTION69
2.7983-2.91030.38831230.36622222X-RAY DIFFRACTION81
2.9103-3.04270.37071280.34332497X-RAY DIFFRACTION91
3.0427-3.20310.35171400.32962641X-RAY DIFFRACTION95
3.2031-3.40370.31081340.30252712X-RAY DIFFRACTION98
3.4037-3.66640.27151440.27112758X-RAY DIFFRACTION99
3.6664-4.03510.30311300.23432793X-RAY DIFFRACTION100
4.0351-4.61840.2311410.19982793X-RAY DIFFRACTION100
4.6184-5.81650.2141340.19012844X-RAY DIFFRACTION100
5.8165-43.58460.22051640.19842946X-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)
11.24380.01230.24350.96310.16641.2566-0.046-0.6461-0.7128-0.26470.08620.08220.3415-0.4474-0.04050.5681-0.0380.00620.27750.31770.6614-1.7919-29.1738-11.2692
21.32030.445-0.09661.3367-0.57892.236-0.27580.3657-0.197-0.40490.16140.1096-0.1907-0.3209-0.04050.6198-0.0766-0.04540.01220.24270.44514.2093-19.8853-26.3515
37.22183.50930.24372.998-0.36612.9003-0.05130.3188-0.82930.07540.383-0.480.220.5553-0.09040.62810.0477-0.06690.24370.03710.527513.8255-19.0912-39.9795
48.37552.2029-0.43352.526-0.57732.6859-0.42031.0302-0.047-0.40240.5113-0.01140.1180.1473-0.02520.6868-0.0751-0.01790.36880.0070.431512.648-16.8256-43.5263
56.15420.7975-2.94321.1233-0.70692.98820.4773-1.59211.190.3157-0.35580.3442-0.67220.3098-0.20310.6788-0.0441-0.04350.6973-0.3080.547311.1785-8.8827-1.0223
69.95830.83184.19499.4155-7.14328.36570.1943-0.03160.0884-0.66830.35410.21330.45750.0216-0.53460.3511-0.02630.03730.2432-0.02940.265412.0216-16.7151-10.4314
75.07080.0618-2.25324.68640.03326.30950.1346-1.95630.28650.9722-0.16-0.26040.10850.43060.00140.4248-0.0578-0.01251.1266-0.04380.472616.3489-16.77891.8654
88.82513.7241-3.56842.8011-1.76124.15810.424-1.64470.61570.3869-0.33680.3429-0.44670.3959-0.16070.3960.0213-0.03730.5116-0.07320.36944.9556-13.7246-4.4385
95.28023.5627-1.14977.4001-1.01640.2645-0.83570.6715-0.2986-1.45880.44220.1315-0.0703-0.030.33441.0307-0.0378-0.06470.25540.05320.61199.9612-4.8682-47.2753
101.5849-0.37460.15331.3954-0.61651.65060.0042-0.23050.8014-0.75020.05550.2165-0.8204-0.2447-0.05460.89030.0932-0.11640.11840.05870.68877.6586-3.8666-36.0515
111.2949-0.63940.30791.495-1.26591.2890.1683-0.22630.6649-0.13750.28-0.6278-0.40890.0692-0.29681.29870.0806-0.33560.123-0.10251.17739.39014.703-36.4383
128.2291-5.13338.95417.2259-6.32262.09180.10940.1217-0.6444-0.4803-0.0463-0.15290.20.1060.05080.6366-0.14520.00741.866-0.03060.498622.648-73.3221-18.0148
136.04430.7132-0.05061.2140.73180.5086-0.107-0.4506-0.04910.0419-0.0730.2543-0.1608-0.52540.22810.4156-0.07610.02181.7410.03790.551317.5523-65.5825-8.4436
141.1096-0.1317-0.39422.054-2.19844.52330.0362-0.6729-0.18330.0488-0.1581-0.01110.0841-0.29020.12990.4268-0.0841-0.03011.4681-0.03760.489723.7585-61.5081-23.3747
156.58663.7921-0.47195.4568-1.65421.20590.2064-0.9312-0.73020.0781-0.6138-1.2895-0.0971.16310.47260.47520.1034-0.02981.11520.06840.653934.4994-54.7238-39.4364
169.11485.99460.21738.2355-1.81255.3287-0.3756-0.3419-0.3363-0.3603-0.1629-0.5195-0.40271.07250.46390.40620.0697-0.04310.755-0.01180.432933.2719-51.8185-42.2385
174.3391.0413-1.59171.1989-0.86992.2497-0.3468-0.49890.80620.16080.0151-0.1205-0.5240.0760.25270.7144-0.1682-0.22191.7405-0.17230.81935.1198-48.4941-3.9959
182.1234-0.44730.09030.5443-0.00981.3262-0.7491-1.0210.22690.73170.0560.0561-0.33180.3380.25840.0711-0.1149-0.07652.36110.02790.565934.381-60.5895-0.1404
193.64370.0521.95571.5471-0.48621.2225-0.5078-0.4840.52260.42610.0763-0.409-0.31280.05160.14020.1446-0.2294-0.4022.4291-0.14230.454738.1229-54.8574-1.2386
205.67251.2598-0.4330.9532-0.44431.23350.2008-0.88820.48860.5132-0.02240.2044-0.3936-0.0316-0.06470.5590.00150.0112.1090.02420.593613.6413-62.59345.4384
210.23480.2671-0.94483.0874-4.17786.4180.0302-0.60960.02620.1099-0.3733-0.3574-0.41050.00230.22410.5555-0.0013-0.12621.3632-0.11020.711533.8422-44.2351-22.4777
221.545-1.6341-0.67774.4802-0.78331.12060.1474-0.8416-0.01840.2539-0.5082-0.0983-0.43570.41850.36870.4085-0.201-0.12541.2256-0.31670.742332.4281-40.6188-34.5543
232.1602-0.8798-0.39734.2183-0.13040.08560.1642-0.9855-0.04260.5432-0.48170.1464-0.29990.54770.30490.6127-0.07960.01681.1611-0.21950.836125.6777-38.9854-27.9143
248.0357-4.66344.12274.9742-1.26215.93440.387-0.96380.3080.1103-0.7443-0.323-0.4718-0.23460.36060.5713-0.1585-0.16121.1233-0.09830.798129.1984-39.8999-33.2844
259.6038-0.0245-6.87656.533-1.7085.3720.2825-0.09091.58141.40280.4708-0.5251-1.24270.971-0.71050.9311-0.1631-0.16520.7167-0.1911.230732.2464-31.2813-30.9895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:75 )A1 - 75
2X-RAY DIFFRACTION2( CHAIN A AND RESID 76:128 )A76 - 128
3X-RAY DIFFRACTION3( CHAIN A AND RESID 129:163 )A129 - 163
4X-RAY DIFFRACTION4( CHAIN A AND RESID 164:212 )A164 - 212
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:33 )B1 - 33
6X-RAY DIFFRACTION6( CHAIN B AND RESID 34:44 )B34 - 44
7X-RAY DIFFRACTION7( CHAIN B AND RESID 45:82 )B45 - 82
8X-RAY DIFFRACTION8( CHAIN B AND RESID 83:119 )B83 - 119
9X-RAY DIFFRACTION9( CHAIN B AND RESID 120:135 )B120 - 135
10X-RAY DIFFRACTION10( CHAIN B AND RESID 136:193 )B136 - 193
11X-RAY DIFFRACTION11( CHAIN B AND RESID 194:214 )B194 - 214
12X-RAY DIFFRACTION12( CHAIN C AND RESID 1:29 )C1 - 29
13X-RAY DIFFRACTION13( CHAIN C AND RESID 30:61 )C30 - 61
14X-RAY DIFFRACTION14( CHAIN C AND RESID 62:128 )C62 - 128
15X-RAY DIFFRACTION15( CHAIN C AND RESID 129:163 )C129 - 163
16X-RAY DIFFRACTION16( CHAIN C AND RESID 164:212 )C164 - 212
17X-RAY DIFFRACTION17( CHAIN D AND RESID 1:17 )D1 - 17
18X-RAY DIFFRACTION18( CHAIN D AND RESID 18:66 )D18 - 66
19X-RAY DIFFRACTION19( CHAIN D AND RESID 67:93 )D67 - 93
20X-RAY DIFFRACTION20( CHAIN D AND RESID 94:100 )D94 - 100
21X-RAY DIFFRACTION21( CHAIN D AND RESID 101:134 )D101 - 134
22X-RAY DIFFRACTION22( CHAIN D AND RESID 135:145 )D135 - 145
23X-RAY DIFFRACTION23( CHAIN D AND RESID 146:165 )D146 - 165
24X-RAY DIFFRACTION24( CHAIN D AND RESID 166:200 )D166 - 200
25X-RAY DIFFRACTION25( CHAIN D AND RESID 201:214 )D201 - 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