[English] 日本語
Yorodumi
- PDB-2w2m: WT PCSK9-DELTAC BOUND TO WT EGF-A OF LDLR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w2m
TitleWT PCSK9-DELTAC BOUND TO WT EGF-A OF LDLR
Components
  • (PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9PCSK9) x 2
  • LOW-DENSITY LIPOPROTEIN RECEPTORLDL receptor
KeywordsHYDROLASE/RECEPTOR / HYDROLASE-RECEPTOR COMPLEX / CARDIOVASCULAR DISEASE / FAMILIAL HYPERCHOLESTEROLEMIA / LIPID METABOLISM / SERINE PROTEASE / LIPID TRANSPORT / STEROID METABOLISM
Function / homology
Function and homology information


regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / very-low-density lipoprotein particle receptor activity / negative regulation of astrocyte activation / negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / receptor-mediated endocytosis involved in cholesterol transport ...regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / very-low-density lipoprotein particle receptor activity / negative regulation of astrocyte activation / negative regulation of low-density lipoprotein particle receptor binding / negative regulation of receptor-mediated endocytosis involved in cholesterol transport / low-density lipoprotein particle receptor catabolic process / extrinsic component of external side of plasma membrane / receptor-mediated endocytosis involved in cholesterol transport / negative regulation of microglial cell activation / very-low-density lipoprotein particle binding / PCSK9-LDLR complex / cholesterol import / negative regulation of receptor recycling / low-density lipoprotein particle clearance / clathrin heavy chain binding / PCSK9-AnxA2 complex / low-density lipoprotein particle receptor activity / negative regulation of sodium ion transmembrane transporter activity / apolipoprotein receptor binding / intestinal cholesterol absorption / positive regulation of triglyceride biosynthetic process / negative regulation of low-density lipoprotein particle clearance / low-density lipoprotein particle binding / response to caloric restriction / Chylomicron clearance / amyloid-beta clearance by cellular catabolic process / LDL clearance / positive regulation of low-density lipoprotein particle receptor catabolic process / lipoprotein metabolic process / signaling receptor inhibitor activity / high-density lipoprotein particle clearance / lipoprotein catabolic process / very-low-density lipoprotein particle receptor binding / regulation of protein metabolic process / low-density lipoprotein particle / phospholipid transport / cholesterol transport / negative regulation of low-density lipoprotein receptor activity / negative regulation of receptor internalization / endolysosome membrane / negative regulation of amyloid fibril formation / regulation of signaling receptor activity / sodium channel inhibitor activity / lysosomal transport / negative regulation of protein metabolic process / artery morphogenesis / triglyceride metabolic process / cellular response to fatty acid / regulation of cholesterol metabolic process / low-density lipoprotein particle receptor binding / COPII-coated ER to Golgi transport vesicle / amyloid-beta clearance / lipoprotein particle binding / sorting endosome / apolipoprotein binding / positive regulation of receptor internalization / cellular response to low-density lipoprotein particle stimulus / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / phospholipid metabolic process / long-term memory / phagocytosis / regulation of neuron apoptotic process / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / VLDLR internalisation and degradation / cellular response to starvation / cholesterol metabolic process / neurogenesis / receptor-mediated endocytosis / liver development / cholesterol homeostasis / kidney development / Post-translational protein phosphorylation / clathrin-coated endocytic vesicle membrane / lipid metabolic process / neuron differentiation / positive regulation of inflammatory response / endocytosis / cellular response to insulin stimulus / positive regulation of neuron apoptotic process / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / : / late endosome / Cargo recognition for clathrin-mediated endocytosis / virus receptor activity / apical part of cell / Clathrin-mediated endocytosis / amyloid-beta binding / basolateral plasma membrane / protease binding / lysosome / molecular adaptor activity / receptor complex / early endosome / endosome membrane / lysosomal membrane
Similarity search - Function
Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1 / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Complement Clr-like EGF-like / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. ...Proprotein convertase subtilisin/kexin type 9, C-terminal domain 3 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 2 / Proprotein convertase subtilisin/kexin type 9, C-terminal domain 1 / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Complement Clr-like EGF-like / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Calcium-binding EGF domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Six-bladed beta-propeller, TolB-like / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / Serine proteases, subtilase domain profile. / EGF-type aspartate/asparagine hydroxylation site / Peptidase S8, subtilisin-related / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Ribbon / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Low-density lipoprotein receptor / Proprotein convertase subtilisin/kexin type 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. ...Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. / Noto, A. / Baysarowich, J. / Mattu, M. / Talamo, F. / De Francesco, R. / Sparrow, C.P. / Sitlani, A. / Carfi, A.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and Biochemical Characterization of the Wild Type Pcsk9/Egf-Ab Complex and Natural Fh Mutants.
Authors: Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. / Noto, A. / Baysarowich, J. / Mattu, M. ...Authors: Bottomley, M.J. / Cirillo, A. / Orsatti, L. / Ruggeri, L. / Fisher, T.S. / Santoro, J.C. / Cummings, R.T. / Cubbon, R.M. / Lo Surdo, P. / Calzetta, A. / Noto, A. / Baysarowich, J. / Mattu, M. / Talamo, F. / De Francesco, R. / Sparrow, C.P. / Sitlani, A. / Carfi, A.
History
DepositionNov 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
E: LOW-DENSITY LIPOPROTEIN RECEPTOR
P: PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0046
Polymers57,8833
Non-polymers1203
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-26.6 kcal/mol
Surface area22230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.004, 83.004, 211.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 / PCSK9 / PROPROTEIN CONVERTASE PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9 / NEURAL APOPTOSIS-REGULATED ...PROPROTEIN CONVERTASE PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9 / NEURAL APOPTOSIS-REGULATED CONVERTASE 1 / NARC-1 / PCSK9


Mass: 33108.227 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 153-451
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein LOW-DENSITY LIPOPROTEIN RECEPTOR / LDL receptor / LDL RECEPTOR


Mass: 12095.453 Da / Num. of mol.: 1 / Fragment: EGF-A DOMAIN, RESIDUES 314-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01130
#3: Protein PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9 / PCSK9 / PROPROTEIN CONVERTASE PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9 / NEURAL APOPTOSIS-REGULATED ...PROPROTEIN CONVERTASE PC9 / SUBTILISIN/KEXIN-LIKE PROTEASE PC9 / NEURAL APOPTOSIS-REGULATED CONVERTASE 1 / NARC-1 / PCSK9


Mass: 12679.604 Da / Num. of mol.: 1 / Fragment: PROPEPTIDE, RESIDUES 53-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM-10 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8NBP7, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN A: HUMAN PCSK9 CATALYTIC DOMAIN. THE LAST 13 RESIDUES ARE A LINKER AND A 6HIS TAG, RESULTING ...CHAIN A: HUMAN PCSK9 CATALYTIC DOMAIN. THE LAST 13 RESIDUES ARE A LINKER AND A 6HIS TAG, RESULTING FROM THE CLONING PROCEDURE. THE FIRST RESIDUE CORRESPONDS TO SER153 OF WT PCSK9. HUMAN LDLR EGF-AB DOMAINS. THE FIRST 27 RESIDUES IN THE SEQUENCE ARE A 6HIS TAG AND A LINKER FROM THE CLONING PROCEDURE. THE 28TH RESIDUE CORRESPONDS TO GLY293 OF WT LDLR. CHAIN P: HUMAN PCSK9 PRODOMAIN. THE FIRST 14 RESIDUES IN THE SEQUENCE ARE A RESULT OF THE CLONING PROCEDURE. THE 15TH RESIDUE CORRESPONDS TO ALA53 OF WT PCSK9.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M HEPES PH 7.5, 10% (V/V) 2-PROPANOL, 20% (W/V) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.4→45 Å / Num. obs: 29902 / % possible obs: 99.9 % / Observed criterion σ(I): 3.5 / Redundancy: 6.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.4
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QTW

2qtw


Resolution: 2.4→45 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.896 / SU B: 12.177 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25421 1512 5.1 %RANDOM
Rwork0.21524 ---
obs0.21719 28296 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.756 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--1.07 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 3 215 3363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223266
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9684448
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3075430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08223.901141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84615535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4631525
X-RAY DIFFRACTIONr_chiral_restr0.0790.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022479
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.21380
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22171
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2172
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4491.52156
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80723374
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.97531228
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6474.51066
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 116
Rwork0.28 2035
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)
10.9680.25691.12670.66850.84733.14790.1142-0.03-0.02130.0767-0.0414-0.05190.2185-0.0483-0.07280.0194-0.048-0.00590.07520.00820.025326.921615.875452.1791
20.9333-0.14630.32780.78080.74641.99750.0435-0.0461-0.0190.0849-0.04340.0430.1824-0.031200.0324-0.01990.00440.0270.01830.017213.0172.242930.3393
32.8012-0.44952.2230.9918-0.55.2985-0.04240.22590.2450.0025-0.1085-0.0198-0.0230.23660.1509-0.03730.030.00480.07990.01720.0368-1.910413.44218.4285
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1P61 - 152
2X-RAY DIFFRACTION2A153 - 447
3X-RAY DIFFRACTION3E285 - 333

+
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