[English] 日本語
Yorodumi
- PDB-6pk8: Antibody scFv-M204 dimeric state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pk8
TitleAntibody scFv-M204 dimeric state
ComponentsscFv-M204 antibody
KeywordsIMMUNE SYSTEM / anti-tau-oligomer scFv antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.91 Å
AuthorsAbskharon, R. / Sawaya, M.R. / Seidler, P.M. / Cascio, D. / Eisenberg, D.S.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R01 AG029430 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)RF1 AG054022 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)1F32 NS095661 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1F32 NS095661 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structure of a conformational antibody that binds tau oligomers and inhibits pathological seeding by extracts from donors with Alzheimer's disease.
Authors: Abskharon, R. / Seidler, P.M. / Sawaya, M.R. / Cascio, D. / Yang, T.P. / Philipp, S. / Williams, C.K. / Newell, K.L. / Ghetti, B. / DeTure, M.A. / Dickson, D.W. / Vinters, H.V. / Felgner, P. ...Authors: Abskharon, R. / Seidler, P.M. / Sawaya, M.R. / Cascio, D. / Yang, T.P. / Philipp, S. / Williams, C.K. / Newell, K.L. / Ghetti, B. / DeTure, M.A. / Dickson, D.W. / Vinters, H.V. / Felgner, P.L. / Nakajima, R. / Glabe, C.G. / Eisenberg, D.S.
History
DepositionJun 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: scFv-M204 antibody
B: scFv-M204 antibody
C: scFv-M204 antibody
D: scFv-M204 antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6328
Polymers108,2484
Non-polymers3844
Water57632
1
A: scFv-M204 antibody
B: scFv-M204 antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3164
Polymers54,1242
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: scFv-M204 antibody
D: scFv-M204 antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3164
Polymers54,1242
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.600, 105.260, 176.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA2 - 2312 - 244
21LYSLYSBB2 - 2312 - 244
12SERSERAA2 - 2322 - 245
22SERSERCC2 - 2322 - 245
13SERSERAA2 - 2322 - 245
23SERSERDD2 - 2322 - 245
14LYSLYSBB2 - 2312 - 244
24LYSLYSCC2 - 2312 - 244
15LYSLYSBB2 - 2312 - 244
25LYSLYSDD2 - 2312 - 244
16SERSERCC2 - 2322 - 245
26SERSERDD2 - 2322 - 245

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Antibody
scFv-M204 antibody


Mass: 27061.957 Da / Num. of mol.: 4 / Fragment: scFv
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pMES4 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.15 M Ammonium sulfate, 0.1 M MES pH 6.0, 15% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.91→90.41 Å / Num. obs: 25041 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Redundancy: 3.73 % / Biso Wilson estimate: 46.195 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.171 / Rrim(I) all: 0.198 / Χ2: 0.954 / Net I/σ(I): 6.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.91-2.993.4750.9751.175737183816510.4811.14489.8
2.99-3.073.8350.8481.476876180117930.5620.98699.6
3.07-3.163.8640.761.696863178017760.6120.88399.8
3.16-3.253.8130.5592.286428169016860.7520.64999.8
3.25-3.363.7640.4782.646301168616740.7920.55699.3
3.36-3.483.7180.3833.335890160215840.8760.44598.9
3.48-3.613.5250.2824.365341156115150.9190.33197.1
3.61-3.763.4060.2075.414980150414620.9570.24497.2
3.76-3.923.9010.1846.665583143414310.9720.21399.8
3.92-4.123.9560.1428.155451138613780.9860.16499.4
4.12-4.343.9280.10410.115197133013230.9940.11999.5
4.34-4.63.8890.09311.664714122612120.9920.10898.9
4.6-4.923.7420.08912.44382118011710.9920.10399.2
4.92-5.313.8270.09811.44198110610970.9940.11399.2
5.31-5.823.7410.10410.593793102610140.9910.12198.8
5.82-6.513.6730.129.6733179309030.9870.13997.1
6.51-7.513.280.1079.8425788377860.990.12593.9
7.51-9.23.8380.06116.0326607046930.9970.07198.4
9.2-13.023.6130.04121.0820275725610.9980.04898.1
13.02-90.413.2660.04318.0410813453310.9980.05295.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å87.67 Å
Translation3.5 Å87.67 Å

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GS3

5gs3


Resolution: 2.91→90.41 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 41.506 / SU ML: 0.331 / SU R Cruickshank DPI: 0.3196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.398
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 2504 10 %RANDOM
Rwork0.1856 ---
obs0.1909 22537 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 136.86 Å2 / Biso mean: 52.733 Å2 / Biso min: 25.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0 Å20 Å2
2--2.44 Å2-0 Å2
3----1.25 Å2
Refinement stepCycle: final / Resolution: 2.91→90.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6789 0 20 32 6841
Biso mean--44.62 41.05 -
Num. residues----899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136977
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176226
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.6539520
X-RAY DIFFRACTIONr_angle_other_deg1.2791.56514482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.865891
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00122.23278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.475151063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2651528
X-RAY DIFFRACTIONr_chiral_restr0.0670.2959
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021483
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A66410.09
12B66410.09
21A67680.07
22C67680.07
31A61270.13
32D61270.13
41B66590.09
42C66590.09
51B60900.14
52D60900.14
61C61130.13
62D61130.13
LS refinement shellResolution: 2.91→2.986 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 164 -
Rwork0.331 1485 -
all-1649 -
obs--89.47 %
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)
10.2343-0.343-0.20540.56110.18860.78250.0247-0.03310.0428-0.10310.0069-0.07110.01090.0026-0.03160.09580.00910.00880.10610.00910.012412.442.44035.3573
20.21640.23190.00030.6486-0.27390.6101-0.0308-0.0302-0.002-0.03350.05220.07130.0020.0389-0.02140.05950.0163-0.01560.10820.01220.02094.625336.143324.578
30.1025-0.16250.05180.60210.180.82280.0421-0.0346-0.0149-0.0156-0.0308-0.0034-0.0845-0.0174-0.01130.0865-0.0066-0.00050.10320.01480.02133.504523.490236.6526
41.3224-0.0137-0.22840.27350.18010.32880.04910.0271-0.103-0.0481-0.0274-0.0002-0.0044-0.0095-0.02160.07520.0087-0.00780.1026-0.01490.017724.482415.177718.7296
50.44010.35250.02650.56570.48260.79010.01160.02810.02710.0681-0.03290.04170.0257-0.06010.02130.1247-0.01360.01120.0995-0.02060.007318.273939.664779.8062
60.11530.19740.02440.62380.51240.78610.00610.01750.0119-0.00750.0611-0.0201-0.00750.0412-0.06730.0605-0.0197-0.01350.109-0.01210.018526.071834.674960.1306
70.22510.30520.01960.492-0.16130.6510.06570.02790.00830.1227-0.01180.0294-0.01860.0213-0.05390.080.01410.00670.10670.00270.0379-2.121622.32346.8466
80.78050.26060.37990.60120.02430.20720.0023-0.0259-0.0720.06340.0277-0.0339-0.0163-0.006-0.030.07380.0001-0.00090.11940.01760.0097.566112.02463.7026
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 119
2X-RAY DIFFRACTION2A120 - 232
3X-RAY DIFFRACTION3B2 - 119
4X-RAY DIFFRACTION4B120 - 232
5X-RAY DIFFRACTION5C2 - 119
6X-RAY DIFFRACTION6C120 - 232
7X-RAY DIFFRACTION7D2 - 119
8X-RAY DIFFRACTION8D120 - 232

+
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