[English] 日本語
Yorodumi
- PDB-6e70: Structure of Wild Type Human Transthyretin in Complex with Diflunisal -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6.0E+70
TitleStructure of Wild Type Human Transthyretin in Complex with Diflunisal
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / human transthyretin / amyloid / transthyretin / diflunisal
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / hormone binding / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family
Similarity search - Domain/homology
5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.992 Å
AuthorsChung, K. / Saelices, L. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG048120 United States
CitationJournal: To Be Published
Title: Structural Variants of Transthyretin
Authors: Saelices, L. / Chung, K. / Esswein, S. / Chou, J. / Liang, W. / Li, J.H. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
History
DepositionJul 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7936
Polymers25,2122
Non-polymers5814
Water59433
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,58612
Polymers50,4244
Non-polymers1,1618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area8790 Å2
ΔGint-79 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.090, 84.320, 65.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

1FL

21B-201-

1FL

31B-201-

1FL

41B-201-

1FL

51B-201-

1FL

61B-201-

1FL

71B-304-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 10 through 33 or resid 35...
21(chain B and (resid 10 through 33 or resid 35...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSPHEPHE(chain A and (resid 10 through 33 or resid 35...AA10 - 331 - 24
12LYSLYSVALVAL(chain A and (resid 10 through 33 or resid 35...AA35 - 7126 - 62
13ILEILETYRTYR(chain A and (resid 10 through 33 or resid 35...AA73 - 11464 - 105
14TYRTYRASNASN(chain A and (resid 10 through 33 or resid 35...AA116 - 124107 - 115
21CYSCYSPHEPHE(chain B and (resid 10 through 33 or resid 35...BB10 - 331 - 24
22LYSLYSVALVAL(chain B and (resid 10 through 33 or resid 35...BB35 - 7126 - 62
23ILEILETYRTYR(chain B and (resid 10 through 33 or resid 35...BB73 - 11464 - 105
24TYRTYRASNASN(chain B and (resid 10 through 33 or resid 35...BB116 - 124107 - 115

-
Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 12606.103 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P02766
#2: Chemical ChemComp-1FL / 5-(2,4-DIFLUOROPHENYL)-2-HYDROXY-BENZOIC ACID / Diflunisal


Mass: 250.198 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H8F2O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% (W/V) PEG-1000, 0.1M Imidazole, 0.2M Calcium Acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.99→65.05 Å / Num. obs: 16279 / % possible obs: 99.1 % / Redundancy: 6.293 % / Biso Wilson estimate: 39.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.076 / Χ2: 0.994 / Net I/σ(I): 13.46 / Num. measured all: 102436
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
1.99-2.045.7950.6882.496143119810600.9090.75488.5
2.04-2.16.3140.5633.37356116811650.9590.61499.7
2.1-2.166.0190.4594.066699111611130.970.50399.7
2.16-2.236.0050.3435.266582109710960.9690.37699.9
2.23-2.36.6560.2766.77062106110610.9880.3100
2.3-2.386.6520.2576.986891103810360.9920.27999.8
2.38-2.476.6520.1978.616719101010100.9940.214100
2.47-2.576.5630.1610.1161369379350.9940.17499.8
2.57-2.696.3270.12712.0959419409390.9930.13999.9
2.69-2.825.8040.10313.7551958978950.9970.11399.8
2.82-2.976.5720.08517.4655478458440.9950.09299.9
2.97-3.156.7210.07120.4153908038020.9940.07799.9
3.15-3.376.6680.06223.3850747617610.9980.068100
3.37-3.646.3970.05725.1145237087070.9980.06299.9
3.64-3.996.040.0526.0939566556550.9980.055100
3.99-4.465.9450.04827.5235736016010.9980.053100
4.46-5.146.5460.04930.1435025355350.9980.054100
5.14-6.36.280.05629.2429394694680.9970.06199.8
6.3-8.915.3530.0626.8319703683680.9970.067100
8.91-65.055.430.0627.6512382282280.9970.067100

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementResolution: 1.992→65.05 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 1622 10 %
Rwork0.1855 14603 -
obs0.19 16225 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.26 Å2 / Biso mean: 50.1335 Å2 / Biso min: 27.6 Å2
Refinement stepCycle: final / Resolution: 1.992→65.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 38 33 1849
Biso mean--86.86 48.62 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061892
X-RAY DIFFRACTIONf_angle_d0.8732588
X-RAY DIFFRACTIONf_chiral_restr0.062288
X-RAY DIFFRACTIONf_plane_restr0.006330
X-RAY DIFFRACTIONf_dihedral_angle_d16.9261102
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1007X-RAY DIFFRACTION9.409TORSIONAL
12B1007X-RAY DIFFRACTION9.409TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9925-2.05110.341180.2791073119189
2.0511-2.11730.2761330.2251191132499
2.1173-2.1930.27281330.21221193132699
2.193-2.28080.25721350.198512111346100
2.2808-2.38460.30191340.20771208134299
2.3846-2.51030.24661350.20212171352100
2.5103-2.66760.28031360.194512201356100
2.6676-2.87360.24521340.210712221356100
2.8736-3.16280.26211350.204612211356100
3.1628-3.62040.20641390.178212501389100
3.6204-4.56110.16051400.151712601400100
4.5611-65.08470.24031500.180813371487100
Refinement TLS params.Method: refined / Origin x: 43.1178 Å / Origin y: 29.3929 Å / Origin z: 81.2155 Å
111213212223313233
T0.2933 Å2-0.0141 Å2-0.0071 Å2-0.2369 Å2-0.0251 Å2--0.3376 Å2
L1.2155 °2-0.1725 °2-0.5941 °2-1.0681 °2-0.2131 °2--1.6062 °2
S-0.0654 Å °0.1214 Å °-0.2899 Å °-0.0592 Å °0.0057 Å °0.0112 Å °0.1441 Å °-0.0504 Å °0.0277 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 124
2X-RAY DIFFRACTION1allB10 - 124
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allD1 - 13
5X-RAY DIFFRACTION1allD14 - 33
6X-RAY DIFFRACTION1allE1 - 2

+
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