[English] 日本語
Yorodumi
- PDB-3cfn: Crystal structure of human transthyretin in complex with 1-anilin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cfn
TitleCrystal structure of human transthyretin in complex with 1-anilino-8-naphthalene sulfonate
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / human transthyretin / amyloid / familial amyloid polyneurophaty / 1 / 8-2AN / Disease mutation / Glycoprotein / Hormone / Polyneuropathy / Retinol-binding / Secreted / Thyroid hormone / Transport / Vitamin A
Function / homology
Function and homology information


Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Transthyretin/hydroxyisourate hydrolase domain / 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 ...Transthyretin/hydroxyisourate hydrolase domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
8-ANILINO-1-NAPHTHALENE SULFONATE / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsLima, L.-M.T.R. / Foguel, D. / Polikarpov, I.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Identification of a novel ligand binding motif in the transthyretin channel.
Authors: Lima, L.M. / Silva, V.D. / Palmieri, L.D. / Oliveira, M.C. / Foguel, D. / Polikarpov, I.
History
DepositionMar 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: 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_initial_refinement_model / struct_ncs_dom_lim / struct_site
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.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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)26,5224
Polymers25,9232
Non-polymers5992
Water3,585199
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0438
Polymers51,8464
Non-polymers1,1974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area5990 Å2
ΔGint-37.6 kcal/mol
Surface area19630 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-10 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.296, 86.497, 63.463
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 5 / Auth seq-ID: 10 - 120 / Label seq-ID: 1 - 111

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Transthyretin / / Prealbumin / TBPA / TTR / ATTR


Mass: 12961.511 Da / Num. of mol.: 2 / Fragment: UNP residue 30-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02766
#2: Chemical ChemComp-2AN / 8-ANILINO-1-NAPHTHALENE SULFONATE / 8-Anilinonaphthalene-1-sulfonic acid


Mass: 299.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13NO3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: mother liquor: 100 mM Tris, pH 7.5, 100 mM KCl, 20 % v/v PEG 400; drop consisting of 1 uL mother liquor and 1 uL wtTTR 10 mg/mL; crystals appeared in about 5 days; complex obtained by ...Details: mother liquor: 100 mM Tris, pH 7.5, 100 mM KCl, 20 % v/v PEG 400; drop consisting of 1 uL mother liquor and 1 uL wtTTR 10 mg/mL; crystals appeared in about 5 days; complex obtained by soaking in mother liquor supplemented with saturating amount of ligand., VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2005 / Details: Osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→51.168 Å / Num. all: 19713 / Num. obs: 19329 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.87-1.966.90.1844.11634523610.18479.8
1.96-2.087.20.1295.81871226110.12993.4
2.08-2.227.30.0928.11813824900.09294.4
2.22-2.47.30.0779.61724123640.07795.1
2.4-2.637.30.05812.81595721820.05895.8
2.63-2.947.30.04316.51455819950.04397
2.94-3.397.30.03120.61310118050.03197.3
3.39-4.167.10.02622.71105515480.02698.3
4.16-5.8870.02420.8869612390.02498.7
5.88-26.256.40.02816.447227340.02898.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.587 / Cor.coef. Fo:Fc: 0.33
Highest resolutionLowest resolution
Rotation3 Å26.25 Å
Translation3 Å26.25 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CFM

3cfm


Resolution: 1.87→26.25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.122 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 994 5.2 %RANDOM
Rwork0.2 ---
all0.203 19713 --
obs0.203 19297 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.107 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.064 Å
Refinement stepCycle: LAST / Resolution: 1.87→26.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 42 199 2019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221984
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9722727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6575252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.3824.04884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65415303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.584159
X-RAY DIFFRACTIONr_chiral_restr0.0690.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021553
X-RAY DIFFRACTIONr_nbd_refined0.1950.2874
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21315
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.221
X-RAY DIFFRACTIONr_mcbond_it0.4811.51256
X-RAY DIFFRACTIONr_mcangle_it0.86221991
X-RAY DIFFRACTIONr_scbond_it0.9853872
X-RAY DIFFRACTIONr_scangle_it1.5224.5736
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
432MEDIUM POSITIONAL0.230.5
395LOOSE POSITIONAL0.625
432MEDIUM THERMAL0.882
395LOOSE THERMAL1.310
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 67 -
Rwork0.22 1238 -
all-1305 -
obs--88.53 %

+
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