[English] 日本語
Yorodumi
- PDB-4ch2: Low-salt crystal structure of a thrombin-GpIbalpha peptide complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ch2
TitleLow-salt crystal structure of a thrombin-GpIbalpha peptide complex
Components
  • PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
  • THROMBIN, HEAVY CHAIN
  • THROMBIN, LIGHT CHAIN
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX
Function / homology
Function and homology information


thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / blood coagulation, intrinsic pathway / Defective F9 activation / Platelet Adhesion to exposed collagen / positive regulation of platelet activation / megakaryocyte development / GP1b-IX-V activation signalling / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / regulation of cytosolic calcium ion concentration / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / release of sequestered calcium ion into cytosol / negative regulation of cytokine production involved in inflammatory response / extracellular matrix / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / lipopolysaccharide binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / cell morphogenesis / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / regulation of cell shape / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / : / positive regulation of cell growth / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / external side of plasma membrane / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : ...Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Kringle-like fold / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Prothrombin / Platelet glycoprotein Ib alpha chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLechtenberg, B.C. / Freund, S.M.V. / Huntington, J.A.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Gpibalpha Interacts Exclusively with Exosite II of Thrombin
Authors: Lechtenberg, B.C. / Freund, S.M.V. / Huntington, J.A.
History
DepositionNov 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Non-polymer description
Revision 1.3Feb 12, 2014Group: Database references
Revision 1.4Dec 20, 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 / 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 / _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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THROMBIN, LIGHT CHAIN
B: THROMBIN, HEAVY CHAIN
C: THROMBIN, LIGHT CHAIN
D: THROMBIN, HEAVY CHAIN
P: PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
Q: PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,94714
Polymers71,6256
Non-polymers1,3228
Water8,521473
1
A: THROMBIN, LIGHT CHAIN
B: THROMBIN, HEAVY CHAIN
P: PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4747
Polymers35,8123
Non-polymers6614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-19.4 kcal/mol
Surface area15360 Å2
MethodPISA
2
C: THROMBIN, LIGHT CHAIN
D: THROMBIN, HEAVY CHAIN
Q: PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4747
Polymers35,8123
Non-polymers6614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-18.4 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.570, 50.560, 76.280
Angle α, β, γ (deg.)90.00, 97.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2196-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUSERSERAA290 - 3156 - 31
21GLUGLUSERSERCC290 - 3156 - 31
12ILEILEGLYGLYBB321 - 5781 - 258
22ILEILEGLYGLYDD321 - 5781 - 258

NCS ensembles :
ID
1
2

-
Components

-
Protein/peptide , 2 types, 4 molecules ACPQ

#1: Protein/peptide THROMBIN, LIGHT CHAIN / COAGULATION FACTOR II


Mass: 4096.534 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET23 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR, PLYSS / References: UniProt: P00734, thrombin
#3: Protein/peptide PLATELET GLYCOPROTEIN IB ALPHA CHAIN, RESIDUES 287-300 / GP-IB ALPHA / GPIB-ALPHA / GPIBA / GLYCOPROTEIN IBALPHA / ANTIGEN CD42B-ALPHA / GPIBALPHA PEPTIDE


Mass: 1935.584 Da / Num. of mol.: 2 / Fragment: C-TERMINAL FRAGMENT OF GPIBALPHA, 271-284 / Source method: obtained synthetically / Details: ALL THREE TYROSINE RESIDUES ARE PHOSPHORYLATED / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P07359

-
Protein , 1 types, 2 molecules BD

#2: Protein THROMBIN, HEAVY CHAIN


Mass: 29780.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET23 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR, PLYSS / References: UniProt: P00734, thrombin

-
Non-polymers , 4 types, 481 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / References: D-Phe-Pro-Arg-CH2Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Nonpolymer detailsDEOXY-CHLOROMETHYL-ARGININE (ACL): MODIFIED BY REACTION WITH CATALYTIC HIS AND SER

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.82 % / Description: NONE
Crystal growpH: 7.4 / Details: 50 MM SODIUM FORMATE, 16% PEG-3350, pH 7.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.6→41.2 Å / Num. obs: 72363 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.8 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PPB

1ppb


Resolution: 1.6→37.1 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.027 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. DISORDERED REGIONS AND SIDE CHAINS ARE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 3646 5 %RANDOM
Rwork0.15452 ---
obs0.15616 68655 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.614 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.14 Å2
2--0.05 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4685 0 86 473 5244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195076
X-RAY DIFFRACTIONr_bond_other_d0.0080.024691
X-RAY DIFFRACTIONr_angle_refined_deg2.0671.9876910
X-RAY DIFFRACTIONr_angle_other_deg1.4113.00310786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1645618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74223.451226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10415825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6321538
X-RAY DIFFRACTIONr_chiral_restr0.1280.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215722
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A10700.12
12C10700.12
21B149300.11
22D149300.11
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 279 -
Rwork0.251 5178 -
obs--98.54 %
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)
112.081-1.3833.84990.2311-1.06036.6807-0.11160.23460.79640.0515-0.0164-0.0908-0.4865-0.03510.1280.1321-0.01030.05250.02880.04650.1562-13.8176-3.5863-1.0791
24.63620.34361.4022.5614-0.21551.1410.0483-0.02150.15890.078-0.0611-0.3395-0.05850.19930.01290.0328-0.0152-0.00390.0611-0.01250.1205-2.8041-9.989710.274
35.58693.89543.39248.08854.60434.86230.00910.1875-0.10070.04540.084-0.51490.20980.2761-0.0930.03550.0265-0.01180.02860.00320.0861-5.0029-23.68798.8133
40.96440.4264-0.12010.92290.13180.56810.0305-0.16390.2330.1143-0.02940.0404-0.0035-0.0665-0.00120.0711-0.0006-0.00210.0689-0.03990.0723-25.9455-9.544815.365
52.10.47250.09361.51010.19760.85070.0532-0.12460.2960.1292-0.0421-0.0258-0.0525-0.0461-0.01110.06960.00750.00480.0198-0.01260.0492-24.0107-6.653511.6069
61.2933-0.0127-0.06320.7916-0.16170.71590.01880.039-0.0385-0.0184-0.0274-0.03840.0496-0.01940.00860.0731-0.0016-0.0040.0343-0.00750.0052-21.1877-22.07137.6016
74.169-2.05882.62372.3793-1.685112.2662-0.2183-0.25730.33920.37180.1121-0.1433-0.51740.25140.10620.1131-0.01240.0220.08-0.02680.0628-70.3917-1.452135.1707
86.4202-0.3975-1.69674.52540.46955.17850.00390.18420.0342-0.00870.06260.349-0.1869-0.247-0.06660.03450.0410.00760.06220.00560.0466-78.822-2.258228.6664
91.4403-0.73230.32517.7792-3.79845.6582-0.05490.0987-0.2549-0.10260.13870.39080.2093-0.2191-0.08380.0242-0.00640.00640.0465-0.0240.0821-77.8921-17.218429.4283
101.2868-0.6637-0.33020.89050.10540.84680.06550.06610.0945-0.0887-0.041-0.1112-0.03540.0511-0.02450.060800.01360.045900.0149-55.2053-7.509423.642
111.0025-0.1831-0.07890.6428-0.05210.64140.00210.0135-0.0729-0.0043-0.0192-0.0271-0.00150.05640.01710.04890.00430.00520.0351-0.01160.0142-58.3389-11.788827.2603
121.3935-0.069-0.05530.6408-0.03480.65390.0117-0.0371-0.19270.0119-0.01680.04930.06680.04220.00510.04750.00480.00840.02050.00010.0323-61.1954-17.19530.8095
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A285 - 292
2X-RAY DIFFRACTION2A293 - 304
3X-RAY DIFFRACTION3A305 - 316
4X-RAY DIFFRACTION4B321 - 384
5X-RAY DIFFRACTION5B385 - 440
6X-RAY DIFFRACTION6B441 - 578
7X-RAY DIFFRACTION7C290 - 297
8X-RAY DIFFRACTION8C298 - 305
9X-RAY DIFFRACTION9C306 - 318
10X-RAY DIFFRACTION10D321 - 373
11X-RAY DIFFRACTION11D374 - 510
12X-RAY DIFFRACTION12D511 - 578

+
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