[English] 日本語
Yorodumi
- PDB-1gqm: The structure of S100A12 in a hexameric form and its proposed rol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gqm
TitleThe structure of S100A12 in a hexameric form and its proposed role in receptor signalling
ComponentsCALGRANULIN C
KeywordsANTIMICROBIAL PROTEIN / S100A12 / S100 PROTEIN FAMILY / EF-HAND / CALCIUM BINDING
Function / homology
Function and homology information


mast cell activation / RAGE receptor binding / monocyte chemotaxis / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / endothelial cell migration / defense response to fungus / xenobiotic metabolic process / neutrophil chemotaxis / positive regulation of MAP kinase activity ...mast cell activation / RAGE receptor binding / monocyte chemotaxis / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / endothelial cell migration / defense response to fungus / xenobiotic metabolic process / neutrophil chemotaxis / positive regulation of MAP kinase activity / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / calcium-dependent protein binding / positive regulation of NF-kappaB transcription factor activity / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / killing of cells of another organism / cytoskeleton / defense response to bacterium / inflammatory response / copper ion binding / innate immune response / calcium ion binding / Neutrophil degranulation / extracellular space / zinc ion binding / extracellular region / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMoroz, O.V. / Antson, A.A. / Dodson, E.G. / Burrel, H.J. / Grist, S.J. / Lloyd, R.M. / Maitland, N.J. / Dodson, G.G. / Wilson, K.S. / Lukanidin, E. / Bronstein, I.B.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: The Structure of S100A12 in a Hexameric Form and its Proposed Role in Receptor Signalling
Authors: Moroz, O.V. / Antson, A.A. / Dodson, E.J. / Burrell, H.J. / Grist, S.J. / Lloyd, R.M. / Maitland, N.J. / Dodson, G.G. / Wilson, K.S. / Lukanidin, E. / Bronstein, I.B.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Human Calcium-Binding Protein S100A12
Authors: Moroz, O.V. / Antson, A.A. / Dodson, G.G. / Wilson, K.S. / Skibshoj, I. / Lukanidin, E. / Bronstein, I.
History
DepositionNov 26, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 28, 2011Group: Atomic model / Derived calculations / Non-polymer description
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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: CALGRANULIN C
B: CALGRANULIN C
C: CALGRANULIN C
D: CALGRANULIN C
E: CALGRANULIN C
F: CALGRANULIN C
G: CALGRANULIN C
H: CALGRANULIN C
I: CALGRANULIN C
J: CALGRANULIN C
K: CALGRANULIN C
L: CALGRANULIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,97348
Polymers125,53012
Non-polymers1,44336
Water46826
1
A: CALGRANULIN C
B: CALGRANULIN C
C: CALGRANULIN C
D: CALGRANULIN C
E: CALGRANULIN C
F: CALGRANULIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,48624
Polymers62,7656
Non-polymers72118
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14080 Å2
ΔGint-279.3 kcal/mol
Surface area23930 Å2
MethodPISA
2
G: CALGRANULIN C
H: CALGRANULIN C
I: CALGRANULIN C
J: CALGRANULIN C
K: CALGRANULIN C
L: CALGRANULIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,48624
Polymers62,7656
Non-polymers72118
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14270 Å2
ΔGint-300 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.875, 100.501, 112.687
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 86
2113B1 - 86
3113C1 - 86
4113D1 - 86
5113E1 - 86
6113F1 - 86
7113G1 - 86
8113H1 - 86
9113I1 - 86
10113J1 - 86
11113K1 - 86
12113L1 - 86
1211A89 - 91
2211B89 - 91
3211C89 - 91
4211D89 - 91
5211E89 - 91
6211F89 - 91
7211G89 - 91
8211H89 - 91
9211I89 - 91
10211J89 - 91
11211K89 - 91
12211L89 - 91

NCS oper:
IDCodeMatrixVector
1given(-0.96225, -0.27215, -0.00047), (-0.27212, 0.96216, -0.01381), (0.00421, -0.01316, -0.9999)0.60899, 0.04408, 0.22707
2given(-0.98229, -0.10796, -0.15316), (-0.07889, -0.50314, 0.8606), (-0.16997, 0.85744, 0.48571)0.70114, -0.33769, 0.20465
3given(0.97363, 0.17264, 0.14911), (0.21673, -0.49604, -0.84082), (-0.0712, 0.85096, -0.52038)0.07775, -0.16776, 0.30557
4given(0.9697, 0.23372, -0.07112), (0.17157, -0.44428, 0.87931), (0.17392, -0.86486, -0.47092)0.10307, -0.37661, 0.01706
5given(-0.99599, -0.03735, 0.08131), (-0.05329, -0.48241, -0.87432), (0.07189, -0.87515, 0.47849)0.62363, -0.1199, -0.07631
6given(0.99911, -0.03936, -0.01517), (-0.01138, -0.59776, 0.8016), (-0.04062, -0.80071, -0.59767)-0.24891, 0.13244, 0.33821
7given(-0.94837, -0.31702, 0.00976), (0.18327, -0.57286, -0.7989), (0.25885, -0.75587, 0.60138)0.28334, 0.3046, 0.16042
8given(0.96411, 0.19765, 0.17728), (-0.21982, 0.96868, 0.11545), (-0.14891, -0.15028, 0.97736)-0.22278, 0.50685, 0.26823
9given(-0.98118, -0.08513, -0.17332), (-0.06224, 0.9891, -0.13346), (0.18279, -0.12016, -0.97578)0.45768, 0.51296, 0.44371
10given(0.95813, 0.25149, -0.13692), (-0.02341, -0.40777, -0.91278), (-0.28539, 0.87777, -0.38481)-0.07415, 0.38463, 0.59298
11given(-0.99327, -0.00407, 0.11571), (0.1088, -0.37465, 0.92076), (0.0396, 0.92716, 0.37257)0.41546, 0.13086, 0.46201

-
Components

#1: Protein
CALGRANULIN C / S100A12 / CAGC / CGRP / NEUTROPHIL S100 PROTEIN / CALCIUM-BINDING PROTEIN IN AMNIOTIC FLUID 1 / CAAF1


Mass: 10460.834 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: GRANULOCYTE / Tissue: BLOOD / References: UniProt: P80511
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.4 Å3/Da / Density % sol: 48.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 20-25% PEG 5K MONOMETHYL ETHER, 0.2M CALCIUM CHLORIDE, 0.1M SODIUM CACODYLATE, HANGING DROP, pH 6.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14-7 mg/mlprotein1drop
210-20 %PEG5000 MME1reservoir
30.2 M1reservoirCaCl2
40.1 Msodium cacodylate1reservoirpH6.5

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorDate: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 32446 / % possible obs: 98.3 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.3 / % possible all: 95.3
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 95.3 % / Num. unique obs: 3107 / Rmerge(I) obs: 0.412

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E8A
Resolution: 2.7→19.84 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.885 / SU B: 14.57 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1029 3.2 %RANDOM
Rwork0.217 ---
obs0.219 31345 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.7→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8440 0 36 26 8502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0218025
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.8611.93410863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.21296
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026030
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3090.34347
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5473
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2170121
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4160.335
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.560.52
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3821.55113
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80628120
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6832912
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8234.52743
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

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A324tight positional0.140.1
2B324tight positional0.140.1
3C324tight positional0.130.1
4D324tight positional0.130.1
5E324tight positional0.130.1
6F324tight positional0.160.1
7G324tight positional0.120.1
8H324tight positional0.140.1
9I324tight positional0.130.1
10J324tight positional0.140.1
11K324tight positional0.130.1
12L324tight positional0.140.1
1A235loose positional0.353
2B235loose positional0.43
3C235loose positional0.383
4D235loose positional0.343
5E235loose positional0.373
6F235loose positional0.393
7G235loose positional0.313
8H235loose positional0.363
9I235loose positional0.393
10J235loose positional0.573
11K235loose positional0.423
12L235loose positional0.533
1A324tight thermal0.150.5
2B324tight thermal0.130.5
3C324tight thermal0.120.5
4D324tight thermal0.130.5
5E324tight thermal0.140.5
6F324tight thermal0.160.5
7G324tight thermal0.140.5
8H324tight thermal0.110.5
9I324tight thermal0.130.5
10J324tight thermal0.120.5
11K324tight thermal0.120.5
12L324tight thermal0.090.5
1A235loose thermal0.411
2B235loose thermal0.491
3C235loose thermal0.361
4D235loose thermal0.431
5E235loose thermal0.391
6F235loose thermal0.461
7G235loose thermal0.41
8H235loose thermal0.371
9I235loose thermal0.411
10J235loose thermal0.441
11K235loose thermal0.381
12L235loose thermal0.311
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.493 65
Rwork0.32 2190
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.87063.8601-0.6179.24411.12644.82570.0811-0.19530.20190.2966-0.28440.8914-0.5127-0.49950.20330.19910.18250.08790.2149-0.04720.38045.7635-1.652116.8516
26.0533-0.5723-1.07046.3117-0.50344.0175-0.0603-0.15480.1639-0.0423-0.0257-0.3651-0.46440.17610.0860.2391-0.0435-0.02810.08210.00180.211325.59191.1658.7835
36.43623.9299-1.58694.295-1.29333.5070.4104-0.6017-0.01690.8783-0.1730.05150.1250.2628-0.23740.36580.0729-0.07910.4850.08540.240227.9693-19.134128.7546
45.09340.66932.30943.9538-0.73218.13790.2473-0.13380.10520.5717-0.33980.25720.67260.24870.09260.30550.03820.13410.34150.10010.27799.3043-28.865723.8453
56.5945-3.1475-0.88036.2556-0.42485.68310.00990.124-0.4243-0.6174-0.10470.6931-0.0116-0.53360.09470.22420.0057-0.17480.1945-0.04470.18979.5313-21.4553-3.5306
65.38850.52381.62358.2010.79735.09820.1137-0.025-0.0591-0.51330.1628-0.66850.16390.2182-0.27650.11630.0760.03640.1247-0.0070.221529.9276-26.49921.4072
76.8874-1.7186-1.83067.68380.60025.6687-0.10240.1534-0.2938-0.49480.21160.29450.5102-0.5415-0.10920.2392-0.0489-0.15750.23310.00030.1572-10.929727.91128.8654
813.0069-0.09032.16215.3748-0.27575.4372-0.007-0.1011-1.5471-0.36130.0332-0.83790.86630.489-0.02620.530.20850.06250.2162-0.02440.43418.651819.497930.6897
96.76661.3738-3.52424.5537-0.54187.0820.6572-0.20510.45460.2579-0.08090.3479-0.81380.0665-0.57630.3307-0.00990.14040.1574-0.08260.2989-5.998350.150645.9722
106.6011-1.483-3.12115.8410.5385.77350.6334-0.17020.2529-0.2871-0.2407-0.4249-0.45331.0277-0.39270.2604-0.06870.08320.3886-0.12410.284412.22547.386234.5421
115.91580.4016-2.21736.0565-2.21248.3966-0.0643-0.8952-0.28790.3506-0.07090.2415-0.010.63180.13520.27720.00120.01280.44940.18530.2218-6.729923.669157.0142
1212.87642.984-5.2534.1277-3.558312.04880.7406-2.9658-0.13770.7909-0.7824-0.6598-0.40812.6670.04180.3654-0.2185-0.13821.44550.09260.342314.377830.048856.2103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION2B1 - 100
3X-RAY DIFFRACTION3C1 - 100
4X-RAY DIFFRACTION4D1 - 100
5X-RAY DIFFRACTION5E1 - 100
6X-RAY DIFFRACTION6F1 - 100
7X-RAY DIFFRACTION7G1 - 100
8X-RAY DIFFRACTION8H1 - 100
9X-RAY DIFFRACTION9I1 - 100
10X-RAY DIFFRACTION10J1 - 100
11X-RAY DIFFRACTION11K1 - 100
12X-RAY DIFFRACTION12L1 - 100
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Rfactor obs: 0.217 / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_d0.0170.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.8611.931
X-RAY DIFFRACTIONr_plane_restr0.0060.02
X-RAY DIFFRACTIONr_chiral_restr0.120.2
LS refinement shell
*PLUS
Rfactor Rwork: 0.32

+
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://pdbjlvh1.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