[English] 日本語
Yorodumi
- PDB-6dcw: Crystal structure of human anti-tau antibody CBTAU-27.1 Fab in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dcw
TitleCrystal structure of human anti-tau antibody CBTAU-27.1 Fab in complex with a human tau peptide
Components
  • Heavy chain of CBTAU27.1 Fab
  • Light chain of CBTAU27.1 Fab
  • tau peptide
KeywordsIMMUNE SYSTEM / Tau / Fab / naturally occurring human antibody / common motif
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / microtubule cytoskeleton organization / neuron projection development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / microtubule binding / Potential therapeutics for SARS / microtubule / adaptive immune response / immune response / axon / dendrite / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol
Similarity search - Function
Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. / : / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Microtubule-associated protein / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhu, X. / Zhang, H. / Wilson, I.A.
CitationJournal: Acta Neuropathol Commun / Year: 2018
Title: A common antigenic motif recognized by naturally occurring human VH5-51/VL4-1 anti-tau antibodies with distinct functionalities.
Authors: Apetri, A. / Crespo, R. / Juraszek, J. / Pascual, G. / Janson, R. / Zhu, X. / Zhang, H. / Keogh, E. / Holland, T. / Wadia, J. / Verveen, H. / Siregar, B. / Mrosek, M. / Taggenbrock, R. / ...Authors: Apetri, A. / Crespo, R. / Juraszek, J. / Pascual, G. / Janson, R. / Zhu, X. / Zhang, H. / Keogh, E. / Holland, T. / Wadia, J. / Verveen, H. / Siregar, B. / Mrosek, M. / Taggenbrock, R. / Ameijde, J. / Inganas, H. / van Winsen, M. / Koldijk, M.H. / Zuijdgeest, D. / Borgers, M. / Dockx, K. / Stoop, E.J.M. / Yu, W. / Brinkman-van der Linden, E.C. / Ummenthum, K. / van Kolen, K. / Mercken, M. / Steinbacher, S. / de Marco, D. / Hoozemans, J.J. / Wilson, I.A. / Koudstaal, W. / Goudsmit, J.
History
DepositionMay 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.pdbx_description / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Light chain of CBTAU27.1 Fab
H: Heavy chain of CBTAU27.1 Fab
T: tau peptide


Theoretical massNumber of molelcules
Total (without water)51,4873
Polymers51,4873
Non-polymers00
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-33 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.308, 59.670, 82.331
Angle α, β, γ (deg.)90.00, 103.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-371-

HOH

21H-301-

HOH

31H-303-

HOH

41H-400-

HOH

-
Components

#1: Antibody Light chain of CBTAU27.1 Fab


Mass: 24432.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293-F / Production host: Homo sapiens (human) / References: UniProt: P01834*PLUS
#2: Antibody Heavy chain of CBTAU27.1 Fab


Mass: 24971.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293-F / Production host: Homo sapiens (human) / References: UniProt: P01857*PLUS
#3: Protein/peptide tau peptide


Mass: 2082.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A0A2K5IAM2*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Hepes, pH 7.0, 0.1 M KCl, 15% PEG5000 MME.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 27347 / % possible obs: 91.5 % / Redundancy: 4 % / CC1/2: 0.99 / Rpim(I) all: 0.06 / Rsym value: 0.11 / Net I/σ(I): 19.5
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 3.5 / Num. unique all: 1223 / CC1/2: 0.784 / Rpim(I) all: 0.25 / Rsym value: 0.38

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QOS

3qos
PDB Unreleased entry


Resolution: 2→43.771 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.67
RfactorNum. reflection% reflection
Rfree0.2156 1384 5.07 %
Rwork0.168 --
obs0.1705 27307 91.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→43.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 0 432 3903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053559
X-RAY DIFFRACTIONf_angle_d0.9374834
X-RAY DIFFRACTIONf_dihedral_angle_d13.6221271
X-RAY DIFFRACTIONf_chiral_restr0.033538
X-RAY DIFFRACTIONf_plane_restr0.004617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9907-2.06190.2511760.21361728X-RAY DIFFRACTION61
2.0619-2.14440.2568980.20382155X-RAY DIFFRACTION76
2.1444-2.2420.25241380.20252634X-RAY DIFFRACTION93
2.242-2.36020.27661620.2142782X-RAY DIFFRACTION98
2.3602-2.50810.27191390.19052762X-RAY DIFFRACTION97
2.5081-2.70170.24871580.19362724X-RAY DIFFRACTION97
2.7017-2.97350.24481580.18952773X-RAY DIFFRACTION98
2.9735-3.40370.2561510.16972750X-RAY DIFFRACTION97
3.4037-4.28770.16871500.13632770X-RAY DIFFRACTION96
4.2877-43.78160.14691540.12622845X-RAY DIFFRACTION97
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)
16.18525.2945-5.14697.1031-5.21024.55240.07990.08810.33430.05160.22280.1963-0.2319-0.2814-0.26240.16390.0099-0.03550.1878-0.01030.14921.497545.237813.6527
26.2421-1.76780.38276.21430.29481.1221-0.07911.1188-0.084-1.1639-0.1829-0.3205-0.26710.17650.20130.3443-0.0568-0.00520.3452-0.00720.17029.978843.9623-5.4764
35.30860.19541.48574.74740.61862.7556-0.0706-0.3763-0.25340.21340.0773-0.25510.3460.1847-0.08890.09080.01290.00470.13260.01230.131112.039837.293815.0989
42.04641.5702-2.74541.2083-2.13367.9991-0.4005-0.0019-0.1626-0.06870.2532-0.0520.391-0.15630.11890.17-0.0673-0.05650.1522-0.02260.15434.914135.6116.7378
50.72140.4064-1.39810.7797-0.71723.6194-0.06120.0118-0.055-0.1311-0.02850.08020.0186-0.03030.06360.0948-0.0104-0.02490.1116-0.00440.11676.281740.947717.643
62.89413.29352.80064.72062.35695.61140.3095-0.0023-0.33240.3158-0.0276-0.62740.33140.6586-0.27630.18110.0136-0.00570.20760.01070.191317.293538.183154.4001
71.53871.19151.55551.94581.70365.21220.0496-0.18690.13060.2595-0.08310.1318-0.2906-0.15370.07130.172-0.02260.03110.1237-0.01160.13346.359845.355247.8712
83.54370.93042.81951.5141.52426.606-0.008-0.11260.12750.17010.0687-0.042-0.12650.1444-0.04160.1267-0.00220.01210.06030.00220.11829.018842.438548.5122
98.52961.42446.92650.75451.80816.87130.3559-0.9372-0.18020.4339-0.18510.1770.3053-0.8707-0.24590.2499-0.12610.06120.3245-0.02710.19251.949239.429255.0118
102.43641.48711.15846.01664.16445.80960.3076-0.0416-0.27170.7535-0.0529-0.57940.50260.1136-0.260.11210.0074-0.05530.1730.00850.214732.061942.814623.3617
111.8830.23170.37691.85140.81813.4021-0.0120.1765-0.0491-0.20420.0793-0.27590.00320.265-0.05710.1185-0.02350.02940.1426-0.01250.146927.776143.295111.5743
121.6431.9725-1.34772.8034-1.95141.97960.0418-0.05630.04260.0992-0.0599-0.0624-0.08680.10530.00720.07910.004-0.02240.1079-0.00140.142119.486638.020341.6627
133.14294.0752-1.23178.5924-3.55351.6850.0182-0.2082-0.2520.1231-0.2901-0.5963-0.09250.22910.29840.1180.0329-0.04040.1694-0.01760.192425.059530.008943.7772
149.4137-2.6545-2.04665.11514.04214.09030.56261.2290.2874-0.9706-0.5434-0.0280.29850.3720.04210.3792-0.03540.06990.333-0.00940.116321.314544.4233-5.714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'L' and (resid 26 through 32 )
3X-RAY DIFFRACTION3chain 'L' and (resid 33 through 48 )
4X-RAY DIFFRACTION4chain 'L' and (resid 49 through 75 )
5X-RAY DIFFRACTION5chain 'L' and (resid 76 through 113 )
6X-RAY DIFFRACTION6chain 'L' and (resid 114 through 128 )
7X-RAY DIFFRACTION7chain 'L' and (resid 129 through 163 )
8X-RAY DIFFRACTION8chain 'L' and (resid 164 through 198 )
9X-RAY DIFFRACTION9chain 'L' and (resid 199 through 213 )
10X-RAY DIFFRACTION10chain 'H' and (resid 1 through 17 )
11X-RAY DIFFRACTION11chain 'H' and (resid 18 through 106 )
12X-RAY DIFFRACTION12chain 'H' and (resid 107 through 197 )
13X-RAY DIFFRACTION13chain 'H' and (resid 198 through 228 )
14X-RAY DIFFRACTION14chain 'T' and (resid 310 through 318 )

+
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