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- PDB-1ob1: Crystal structure of a Fab complex whith Plasmodium falciparum MSP1-19 -

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Basic information

Entry
Database: PDB / ID: 1ob1
TitleCrystal structure of a Fab complex whith Plasmodium falciparum MSP1-19
Components
  • ANTIBODY, HEAVY CHAIN
  • ANTIBODY, LIGHT CHAIN
  • MAJOR MEROZOITE SURFACE PROTEIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN-COMPLEX / IMMUNOGLOBULIN / ANTIBODY FAB FRAGMENT / MSP1-19 / EGF-LIKE DOMAIN / SURFACE ANTIGEN / MALARIA VACCINE COMPONENT
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / : / complement activation, classical pathway / antigen binding / antibacterial humoral response / membrane => GO:0016020 / extracellular space / plasma membrane
Similarity search - Function
Merozoite surface 1, C-terminal / Merozoite surface protein, EGF domain 1 / Merozoite surface protein 1 (MSP1) C-terminus / MSP1 EGF domain 1 / Laminin / Laminin / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ribbon ...Merozoite surface 1, C-terminal / Merozoite surface protein, EGF domain 1 / Merozoite surface protein 1 (MSP1) C-terminus / MSP1 EGF domain 1 / Laminin / Laminin / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ribbon / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CACODYLATE ION / LOC100046793 protein / Ig gamma-2A chain C region, A allele / Merozoite surface antigens
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPizarro, J.C. / Chitarra, V. / Verger, D. / Holm, I. / Petres, S. / Dartville, S. / Nato, F. / Longacre, S. / Bentley, G.A.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of a Fab Complex Formed with Pfmsp1-19, the C-Terminal Fragment of Merozoite Surface Protein 1 from Plasmodium Falciparum: A Malaria Vaccine Candidate
Authors: Pizarro, J.C. / Chitarra, V. / Verger, D. / Holm, I. / Petres, S. / Dartville, S. / Nato, F. / Longacre, S. / Bentley, G.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary Structural Analysis of an Antibody Complex Formed with Pfmsp1-19, a Malaria Vaccine Candidate
Authors: Pizarro, J.C. / Chitarra, V. / Calvet, C. / Verger, D. / Bentley, G.A.
History
DepositionJan 22, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / 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_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
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 / _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
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIBODY, HEAVY CHAIN
B: ANTIBODY, LIGHT CHAIN
C: MAJOR MEROZOITE SURFACE PROTEIN
D: ANTIBODY, HEAVY CHAIN
E: ANTIBODY, LIGHT CHAIN
F: MAJOR MEROZOITE SURFACE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2648
Polymers116,9906
Non-polymers2742
Water0
1
A: ANTIBODY, HEAVY CHAIN
B: ANTIBODY, LIGHT CHAIN
C: MAJOR MEROZOITE SURFACE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6324
Polymers58,4953
Non-polymers1371
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-28.6 kcal/mol
Surface area24760 Å2
MethodPISA
2
D: ANTIBODY, HEAVY CHAIN
E: ANTIBODY, LIGHT CHAIN
F: MAJOR MEROZOITE SURFACE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6324
Polymers58,4953
Non-polymers1371
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-28.9 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.750, 213.460, 59.890
Angle α, β, γ (deg.)90.00, 100.95, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13A
23D
14B
24E
15C
25F

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEGLNGLNAA10 - 3810 - 39
211ILEILEGLNGLNDD10 - 3810 - 39
121PROPROILEILEAA44 - 7545 - 76
221PROPROILEILEDD44 - 7545 - 76
131ASPASPARGARGAA82 - 10783 - 109
231ASPASPARGARGDD82 - 10783 - 109
112GLUGLUVALVALBB1 - 371 - 37
212GLUGLUVALVALEE1 - 371 - 37
122ASPASPASPASPBB44 - 10144 - 108
222ASPASPASPASPEE44 - 10144 - 108
132TRPTRPALAALABB103 - 118110 - 125
232TRPTRPALAALAEE103 - 118110 - 125
113THRTHRPHEPHEAA113 - 138115 - 140
213THRTHRPHEPHEDD113 - 138115 - 140
123ILEILEASNASNAA149 - 211151 - 213
223ILEILEASNASNDD149 - 211151 - 213
114LEULEUTHRTHRBB124 - 131131 - 138
214LEULEUTHRTHREE124 - 131131 - 138
124LEULEUPROPROBB141 - 212148 - 219
224LEULEUPROPROEE141 - 212148 - 219
115GLNGLNTHRTHRCC6 - 636 - 63
215GLNGLNTHRTHRFF6 - 636 - 63
125ILEILESERSERCC74 - 9374 - 93
225ILEILESERSERFF74 - 9374 - 93

NCS ensembles :
ID
1
2
3
4
5
DetailsONE TRIMER IS MADE UP OF HEAVY CHAIN A LIGHT CHAIN BAND MEROZOITE SURFACE PROTEIN 1 CHAIN C. THE OTHER TRIMER IS MADE UP OF HEAVY CHAIN D LIGHTCHAIN E AND MEROZOITE SURFACE PROTEIN 1 CHAIN FTHE CHAIN IN THE COMPLEX A, B, C IS 1691.4 ANGSTROM**2THE CHAIN IN THE COMPLEX D, E, F IS 1666.6 ANGSTROM**2

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Components

#1: Antibody ANTIBODY, HEAVY CHAIN /


Mass: 23659.107 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-LYMPHOCYTE / Cell line: G17-12 MURINE HYBRIDOMA / Strain: BALB/C / References: UniProt: A0A5E3*PLUS
#2: Antibody ANTIBODY, LIGHT CHAIN /


Mass: 23650.516 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-LYMPHOCYTE / Cell line: G17-12 MURINE HYBRIDOMA / Strain: BALB/C / References: UniProt: P01863*PLUS
#3: Protein MAJOR MEROZOITE SURFACE PROTEIN


Mass: 11185.328 Da / Num. of mol.: 2 / Fragment: MSP1-19, RESIDUES 8-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: UGANDA PALO ALTO / Description: SYNTHETIC GENE / Cell: MEROZOITE STAGE / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q25976
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
Sequence detailsANTIBODY RESIDUE NUMBERING FOLLOWS THE KABAT CONVENTION (E.A.KABAT,T.T.WU, M.REID-MILLER, H.M. ...ANTIBODY RESIDUE NUMBERING FOLLOWS THE KABAT CONVENTION (E.A.KABAT,T.T.WU, M.REID-MILLER, H.M.PERRY, A K.S.GOTTESMAN (1991) SEQUENCES OF PROTEINS OF IMMUNOLOGIC INTEREST, 5TH ED., NATIONAL INSTITUTES OF HEALTH BETHESDA) CHAINS A AND C HAVE A C-TERMINAL SIX RESIDUE HIS TAG

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.5
Details: 0.075M SODIUM ACETATE 0.038M SODIUM CACODYLATE, 11.3% PEG8000, 3% DIOXANE, pH 6.50
Crystal grow
*PLUS
Temperature: 291 K / pH: 7.4 / Method: vapor diffusion
Details: Pizarro, J.C., (2001) Acta Crystallogr.,Sect.D, D58, 1246.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
210 mMTris1droppH7.4
30.075 Msodium acetate1reservoir
40.038 Msodium cacodylate1reservoir
511.3 %PEG80001reservoir
63 %dioxane1reservoirpH6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 27530 / % possible obs: 96.8 % / Redundancy: 3.39 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.5
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.6 / % possible all: 87.6
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 3.34 %
Reflection shell
*PLUS
% possible obs: 87.6 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2IGF, 1A3R, 1B9W
Resolution: 2.9→105.41 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.854 / SU B: 21.27 / SU ML: 0.416 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1368 5 %RANDOM
Rwork0.257 ---
obs0.258 25850 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å21.44 Å2
2--3.19 Å20 Å2
3----4.27 Å2
Refinement stepCycle: LAST / Resolution: 2.9→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8132 0 10 0 8142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0218362
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.2671.93711376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.52931053
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.478151450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.21250
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026355
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2920.33900
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.5761
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3630.341
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3110.53
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1871.55276
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.35528549
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.67333086
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0834.52827
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A418tight positional0.030.05
12D418tight positional0.030.05
21B1294tight positional0.040.05
22E1294tight positional0.040.05
31A1981tight positional0.020.05
32D1981tight positional0.020.05
41B2567tight positional0.010.05
42E2567tight positional0.010.05
51C3167tight positional0.010.05
52F3167tight positional0.010.05
11A252loose positional0.235
12D252loose positional0.235
21B252loose positional0.035
22E252loose positional0.035
31A252loose positional0.015
32D252loose positional0.015
41B252loose positional0.015
42E252loose positional0.015
51C252loose positional0.015
52F252loose positional0.015
11A418tight thermal0.070.5
12D418tight thermal0.070.5
21B1294tight thermal0.570.5
22E1294tight thermal0.570.5
31A1981tight thermal1.340.5
32D1981tight thermal1.340.5
41B2567tight thermal1.80.5
42E2567tight thermal1.80.5
51C3167tight thermal1.880.5
52F3167tight thermal1.880.5
11A252loose thermal0.810
12D252loose thermal0.810
21B252loose thermal4.4410
22E252loose thermal4.4410
31A252loose thermal10.4710
32D252loose thermal10.4710
41B252loose thermal16.110
42E252loose thermal16.110
51C252loose thermal19.9610
52F252loose thermal19.9610
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.384 89
Rwork0.33 1731
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)
15.00570.3025-0.21213.30091.66648.4040.00770.309-0.2376-0.1216-0.44830.4766-0.2873-0.80880.44060.01520.0624-0.06290.3982-0.14760.34640.37118.255410.5924
28.24471.460.68278.72242.54066.59140.3876-0.6468-1.82130.999-0.26190.59931.81-0.261-0.12560.8984-0.0277-0.05710.38160.19620.69517.3157-8.429623.7657
34.4674-0.9736-1.49635.56593.711710.33240.0133-0.08660.7714-0.8458-0.25580.3867-2.5565-0.90280.24250.91710.14290.01660.3222-0.12080.503810.673135.704523.6276
47.607-0.24630.510910.55472.72757.80890.4265-0.05271.9867-1.18070.5583-1.4343-3.0321.5647-0.98481.5334-0.7470.59240.8241-0.33070.97631.039639.771615.4681
54.747-0.76343.02139.85636.328510.40880.1643-0.04390.09920.59310.2966-0.7457-0.24251.21-0.46090.5654-0.1636-0.04560.7528-0.02310.2619.702516.863338.2882
65.0269-0.71031.205910.99897.01469.846-0.15740.2323-0.3723-0.01470.715-0.396-0.3760.4992-0.55760.238-0.21240.14890.5717-0.09470.251623.831111.7372.1529
79.59695.4551-0.631620.0774-1.96226.1167-1.07861.4617-1.7848-1.5121.66481.21371.7103-1.2764-0.58620.8079-0.4269-0.1411.587-0.55371.3164-17.163-17.4107-9.3258
812.78367.0558-0.142926.5103-6.835718.4233-0.01722.0836-5.053-1.2832-0.3395-4.7682.80271.27590.35670.93310.12370.21741.0957-1.03263.276-2.7904-23.5546-6.1193
946.524446.5358-13.446367.51-15.37836.52475.13440.798410.51787.9676-0.47229.1753-3.6638-0.1382-4.66223.66910.34241.2920.694-0.3523.395414.213368.809140.5997
1028.41846.75470.00214.8233-5.4058.49091.6163-3.34510.57912.45070.1289-2.7167-2.79131.2965-1.74522.8553-0.1859-0.6890.9111-0.54262.332228.587261.37141.7156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 110
2X-RAY DIFFRACTION2B1 - 120
3X-RAY DIFFRACTION3D1 - 110
4X-RAY DIFFRACTION4E1 - 120
5X-RAY DIFFRACTION5C1 - 95
6X-RAY DIFFRACTION5C1096
7X-RAY DIFFRACTION6F1 - 96
8X-RAY DIFFRACTION6F1097
9X-RAY DIFFRACTION7A111 - 215
10X-RAY DIFFRACTION8B121 - 219
11X-RAY DIFFRACTION9D111 - 215
12X-RAY DIFFRACTION10E121 - 219
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.258 / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.008
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3
X-RAY DIFFRACTIONr_plane_restr0.005
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 2.98 Å / Rfactor Rwork: 0.33

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