[English] 日本語
Yorodumi
- PDB-3lrs: Structure of PG16, an antibody with broad and potent neutralizati... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lrs
TitleStructure of PG16, an antibody with broad and potent neutralization of HIV-1
Components
  • PG-16 Heavy Chain Fab
  • PG-16 Light Chain Fab
KeywordsIMMUNE SYSTEM / neutralizing antibodies / long CDRH3 / HIV-1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsPancera, M. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2010
Title: Crystal structure of PG16 and chimeric dissection with somatically related PG9: structure-function analysis of two quaternary-specific antibodies that effectively neutralize HIV-1.
Authors: Pancera, M. / McLellan, J.S. / Wu, X. / Zhu, J. / Changela, A. / Schmidt, S.D. / Yang, Y. / Zhou, T. / Phogat, S. / Mascola, J.R. / Kwong, P.D.
History
DepositionFeb 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: PG-16 Heavy Chain Fab
L: PG-16 Light Chain Fab
A: PG-16 Heavy Chain Fab
B: PG-16 Light Chain Fab
C: PG-16 Heavy Chain Fab
D: PG-16 Light Chain Fab
E: PG-16 Heavy Chain Fab
F: PG-16 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,21912
Polymers192,3348
Non-polymers8854
Water7,008389
1
H: PG-16 Heavy Chain Fab
L: PG-16 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3053
Polymers48,0842
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-21 kcal/mol
Surface area18970 Å2
MethodPISA
2
A: PG-16 Heavy Chain Fab
B: PG-16 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3053
Polymers48,0842
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-21 kcal/mol
Surface area19300 Å2
MethodPISA
3
C: PG-16 Heavy Chain Fab
D: PG-16 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3053
Polymers48,0842
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-20 kcal/mol
Surface area19500 Å2
MethodPISA
4
E: PG-16 Heavy Chain Fab
F: PG-16 Light Chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3053
Polymers48,0842
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-20 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.317, 165.085, 81.363
Angle α, β, γ (deg.)90.00, 91.55, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody
PG-16 Heavy Chain Fab


Mass: 25919.049 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Organ (production host): KIDNEY / Production host: Homo sapiens (human)
#2: Antibody
PG-16 Light Chain Fab


Mass: 22164.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): HEK 293F / Organ (production host): KIDNEY / Production host: Homo sapiens (human)
#3: 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.: 4
Source method: isolated from a genetically manipulated source
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 293 K / pH: 10.5
Details: 0.74M Potassium Dihydrogen Phosphate, 1.10M Sodium Dihydrogen Phosphate, 0.2M Lithium Sulfate Monohydrate, 0.1 M CAPS, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 71375 / % possible obs: 81.5 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.126 / Rsym value: 0.099 / Net I/σ(I): 15.73
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5116 / Mean I/σ(I) obs: 1.49 / Rsym value: 0.514 / % possible all: 25.4

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NLO

1nlo


Resolution: 2.37→30.59 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 3598 5.04 %
Rwork0.211 --
obs0.213 71375 82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.03 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 65.38 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å2-0 Å2-8.961 Å2
2---2.786 Å2-0 Å2
3----0.364 Å2
Refinement stepCycle: LAST / Resolution: 2.37→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12979 0 56 389 13424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813375
X-RAY DIFFRACTIONf_angle_d1.15418170
X-RAY DIFFRACTIONf_dihedral_angle_d16.0984677
X-RAY DIFFRACTIONf_chiral_restr0.0682041
X-RAY DIFFRACTIONf_plane_restr0.0052317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.3990.427410.265902X-RAY DIFFRACTION28
2.399-2.4320.358580.261252X-RAY DIFFRACTION40
2.432-2.4660.327900.261384X-RAY DIFFRACTION43
2.466-2.5030.352810.2761522X-RAY DIFFRACTION49
2.503-2.5420.332960.2751750X-RAY DIFFRACTION54
2.542-2.5840.3631060.2641857X-RAY DIFFRACTION60
2.584-2.6280.3311250.2612081X-RAY DIFFRACTION65
2.628-2.6760.2951020.2792197X-RAY DIFFRACTION71
2.676-2.7280.3511270.2742424X-RAY DIFFRACTION75
2.728-2.7830.3431360.2722520X-RAY DIFFRACTION80
2.783-2.8440.3481360.2572716X-RAY DIFFRACTION86
2.844-2.910.2871440.2582956X-RAY DIFFRACTION91
2.91-2.9830.3131450.2483023X-RAY DIFFRACTION96
2.983-3.0630.3061600.2483103X-RAY DIFFRACTION98
3.063-3.1530.3131700.2353152X-RAY DIFFRACTION99
3.153-3.2550.2841700.2283172X-RAY DIFFRACTION100
3.255-3.3710.2661640.2143153X-RAY DIFFRACTION100
3.371-3.5060.2991750.2033162X-RAY DIFFRACTION100
3.506-3.6650.2611830.1863154X-RAY DIFFRACTION99
3.665-3.8580.2211400.193197X-RAY DIFFRACTION100
3.858-4.0990.2371810.1663159X-RAY DIFFRACTION100
4.099-4.4150.1851710.1443146X-RAY DIFFRACTION100
4.415-4.8580.1931840.143198X-RAY DIFFRACTION100
4.858-5.5570.2051770.1583186X-RAY DIFFRACTION100
5.557-6.9880.31590.2043205X-RAY DIFFRACTION100
6.988-30.5930.2211770.2213206X-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)
12.7617-0.4191.65830.6889-0.10981.5554-0.14770.06590.2459-0.40850.1581-0.024-0.3473-0.130.00590.51890.0654-0.04320.2612-0.02730.2405-20.9146-11.5481-24.6659
22.0461.12570.11723.49630.440.20690.3788-0.7203-0.121.1481-0.45430.1546-0.0507-0.07870.01750.6956-0.10060.09880.4611-0.0840.1189-33.0956-38.8584-24.4563
33.7274-0.04661.56821.98350.13993.03280.35860.10350.1089-0.0951-0.1239-0.22280.250.1679-0.21860.4452-0.0128-0.02920.2816-0.0390.3487-3.1257-21.1064-17.3239
45.10432.0483-1.98891.2039-1.1931.19760.5426-0.7636-0.23080.5414-0.3843-0.1539-0.26040.3-0.07070.5139-0.011-0.17820.3887-0.08470.2356-24.4448-49.6801-33.4941
51.28960.1322.05911.38580.73553.25470.17430.1099-0.1064-0.11330.00440.43490.3116-0.021-0.12810.29640.0302-0.04080.2723-0.04760.410417.6751-66.0202-62.2785
60.73170.72551.05772.9911-0.80872.10620.14360.3050.1930.0402-0.3974-0.6813-0.03760.81320.30380.18550.04360.10080.53840.04270.724618.2682-38.7141-74.4006
72.70540.0011.6212.54550.44192.9454-0.3247-0.2040.17510.42970.04030.0130.1946-0.15670.23430.42520.03920.01260.36440.00910.289424.501-56.4714-44.269
82.23481.0227-0.98641.4991-2.70284.37040.0793-0.2355-0.41750.184-0.3903-0.4905-0.05020.62140.26290.34260.0994-0.18090.4120.01810.47249.0307-27.9312-66.225
92.889-0.0396-1.7880.44790.75331.4078-0.1468-0.0593-0.081-0.03010.33440.04810.1901-0.0706-0.08660.45070.0751-0.04980.297-0.00690.2663-17.9234-24.6881-65.3901
101.1492-0.6758-0.07765.1109-0.54440.0826-0.0854-0.14690.19260.6650.0729-0.0697-0.3550.3331-0.05080.7532-0.0291-0.08830.3397-0.04560.2585-3.21952.3814-64.8765
111.98241.8518-2.10243.2965-1.37034.680.23840.19580.1420.02810.09460.4562-0.3673-0.3069-0.31990.3331-0.0107-0.01060.30270.03650.3191-35.5592-14.8063-58.539
124.87732.7920.60271.2808-0.03772.9610.4444-0.33330.45240.3978-0.0250.3630.1258-0.4397-0.33560.4738-0.00480.15230.35550.13660.3273-11.181413.4095-73.6186
132.1745-0.7393-2.04010.01120.17022.3995-0.21-0.13430.1257-0.01520.246-0.1214-0.0840.0343-0.03830.277-0.0098-0.05160.2936-0.06920.3262-23.1132-52.8585-60.345
140.9704-0.2008-0.28914.61520.89721.30240.0132-0.08-0.11510.1941-0.0622-0.73990.18260.09080.06360.26110.0254-0.09710.3010.03640.5835-22.961-79.9321-45.5817
154.65111.0445-2.02352.7707-1.42851.1971-0.36530.3277-0.3638-0.54240.189-0.05550.0666-0.2740.17830.4666-0.0571-0.00790.3324-0.01360.2825-15.7998-62.7513-77.7682
165.99841.8823-0.51271.5785-2.67184.7961-0.48830.5025-0.0357-0.3414-0.0183-0.1140.63320.28490.4490.4252-0.1190.15570.35190.03560.3246-31.3674-91.149-54.8834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN L AND RESID 1:112
2X-RAY DIFFRACTION2CHAIN L AND RESID 113:213
3X-RAY DIFFRACTION3CHAIN H AND RESID 1:137
4X-RAY DIFFRACTION4CHAIN H AND RESID 138:239
5X-RAY DIFFRACTION5CHAIN B AND RESID 1:112
6X-RAY DIFFRACTION6CHAIN B AND RESID 113:213
7X-RAY DIFFRACTION7CHAIN A AND RESID 1:137
8X-RAY DIFFRACTION8CHAIN A AND RESID 138:239
9X-RAY DIFFRACTION9CHAIN D AND RESID 1:112
10X-RAY DIFFRACTION10CHAIN D AND RESID 113:213
11X-RAY DIFFRACTION11CHAIN C AND RESID 1:137
12X-RAY DIFFRACTION12CHAIN C AND RESID 138:239
13X-RAY DIFFRACTION13CHAIN F AND RESID 1:112
14X-RAY DIFFRACTION14CHAIN F AND RESID 113:213
15X-RAY DIFFRACTION15CHAIN E AND RESID 1:137
16X-RAY DIFFRACTION16CHAIN E AND RESID 138:239

+
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