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- PDB-3nk3: Crystal structure of full-length sperm receptor ZP3 at 2.6 A reso... -

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Basic information

Entry
Database: PDB / ID: 3nk3
TitleCrystal structure of full-length sperm receptor ZP3 at 2.6 A resolution
Components(Zona pellucida 3) x 2
KeywordsCELL ADHESION / FERTILIZATION / OOCYTE / EGG COAT / ZONA PELLUCIDA / VITELLINE ENVELOPE / ZP DOMAIN / ZP MODULE / EGG-SPERM INTERACTION / SPECIES-SPECIFIC GAMETE RECOGNITION / SPECIATION / BIODIVERSITY / INFERTILITY / EXTRACELLULAR MATRIX / IMMUNOGLOBULIN-LIKE FOLD / GLYCOPROTEIN / RECEPTOR / SECRETED / TRANSMEMBRANE / O-LINKED CARBOHYDRATE / T-ANTIGEN / CORE-1 / EXTERNAL HYDROPHOBIC PATCH / EHP / INTERNAL HYDROPHOBIC PATCH / IHP / SPERM-COMBINING SITE
Function / homology
Function and homology information


egg coat formation / structural constituent of egg coat / acrosin binding / positive regulation of acrosome reaction / binding of sperm to zona pellucida / response to testosterone / extracellular matrix / response to progesterone / apical part of cell / extracellular space ...egg coat formation / structural constituent of egg coat / acrosin binding / positive regulation of acrosome reaction / binding of sperm to zona pellucida / response to testosterone / extracellular matrix / response to progesterone / apical part of cell / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
Zona pellucida, ZP-N domain / Zona pellucida, ZP-C domain / : / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain ...Zona pellucida, ZP-N domain / Zona pellucida, ZP-C domain / : / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Thomsen-Friedenreich antigen / CITRATE ANION / Zona pellucida sperm-binding protein 3
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMonne, M. / Jovine, L.
Citation
Journal: Cell / Year: 2010
Title: Insights into egg coat assembly and egg-sperm interaction from the X-ray structure of full-length ZP3.
Authors: Ling Han / Magnus Monné / Hiroki Okumura / Thomas Schwend / Amy L Cherry / David Flot / Tsukasa Matsuda / Luca Jovine /
Abstract: ZP3, a major component of the zona pellucida (ZP) matrix coating mammalian eggs, is essential for fertilization by acting as sperm receptor. By retaining a propeptide that contains a polymerization- ...ZP3, a major component of the zona pellucida (ZP) matrix coating mammalian eggs, is essential for fertilization by acting as sperm receptor. By retaining a propeptide that contains a polymerization-blocking external hydrophobic patch (EHP), we determined the crystal structure of an avian homolog of ZP3 at 2.0 Å resolution. The structure unveils the fold of a complete ZP domain module in a homodimeric arrangement required for secretion and reveals how EHP prevents premature incorporation of ZP3 into the ZP. This suggests mechanisms underlying polymerization and how local structural differences, reflected by alternative disulfide patterns, control the specificity of ZP subunit interaction. Close relative positioning of a conserved O-glycan important for sperm binding and the hypervariable, positively selected C-terminal region of ZP3 suggests a concerted role in the regulation of species-restricted gamete recognition. Alternative conformations of the area around the O-glycan indicate how sperm binding could trigger downstream events via intramolecular signaling.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1980
Title: Mammalian Sperm-Egg Interaction: Identification of a Glycoprotein in Mouse Egg Zonae Pellucidae Possessing Receptor Activity for Sperm
Authors: Bleil, J.D. / Wassarman, P.M.
#2: Journal: FEBS Lett. / Year: 1992
Title: A Large Domain Common to Sperm Receptors (Zp2 and Zp3) and Tgf-Beta Type III Receptor
Authors: Bork, P. / Sander, C.
#3: Journal: Biol. Reprod. / Year: 1998
Title: The chicken homologue of zona pellucida protein-3 is synthesized by granulosa cells
Authors: Waclawek, M. / Foisner, R. / Nimpf, J. / Schneider, W.J.
#4: Journal: Eur.J.Biochem. / Year: 1999
Title: A 42-kDa Glycoprotein from Chicken Egg-Envelope, an Avian Homolog of the Zpc Family Glycoproteins in Mammalian Zona Pellucida. Its First Identification, Cdna Cloning and Granulosa Cell-Specific Expression.
Authors: Takeuchi, Y. / Nishimura, K. / Aoki, N. / Adachi, T. / Sato, C. / Kitajima, T. / Matsuda, T.
#5: Journal: Nat Cell Biol / Year: 2002
Title: The ZP domain is a conserved module for polymerization of extracellular proteins.
Authors: Luca Jovine / Huayu Qi / Zev Williams / Eveline Litscher / Paul M Wassarman /
Abstract: Many eukaryotic extracellular proteins share a sequence of unknown function, called the zona pellucida (ZP) domain. Among these proteins are the mammalian sperm receptors ZP2 and ZP3, non-mammalian ...Many eukaryotic extracellular proteins share a sequence of unknown function, called the zona pellucida (ZP) domain. Among these proteins are the mammalian sperm receptors ZP2 and ZP3, non-mammalian egg coat proteins, Tamm-Horsfall protein (THP), glycoprotein-2 (GP-2), alpha- and beta-tectorins, transforming growth factor (TGF)-beta receptor III and endoglin, DMBT-1 (deleted in malignant brain tumour-1), NompA (no-mechanoreceptor-potential-A), Dumpy and cuticlin-1 (refs 1,2). Here, we report that the ZP domain of ZP2, ZP3 and THP is responsible for polymerization of these proteins into filaments of similar supramolecular structure. Most ZP domain proteins are synthesized as precursors with carboxy-terminal transmembrane domains or glycosyl phosphatidylinositol (GPI) anchors. Our results demonstrate that the C-terminal transmembrane domain and short cytoplasmic tail of ZP2 and ZP3 are not required for secretion, but are essential for assembly. Finally, we suggest a molecular basis for dominant human hearing disorders caused by point mutations within the ZP domain of alpha-tectorin.
#6: Journal: Proc Natl Acad Sci U S A / Year: 2004
Title: A duplicated motif controls assembly of zona pellucida domain proteins.
Authors: Luca Jovine / Huayu Qi / Zev Williams / Eveline S Litscher / Paul M Wassarman /
Abstract: Many secreted eukaryotic glycoproteins that play fundamental roles in development, hearing, immunity, and cancer polymerize into filaments and extracellular matrices through zona pellucida (ZP) ...Many secreted eukaryotic glycoproteins that play fundamental roles in development, hearing, immunity, and cancer polymerize into filaments and extracellular matrices through zona pellucida (ZP) domains. ZP domain proteins are synthesized as precursors containing C-terminal propeptides that are cleaved at conserved sites. However, the consequences of this processing and the mechanism by which nascent proteins assemble are unclear. By microinjection of mutated DNA constructs into growing oocytes and mammalian cell transfection, we have identified a conserved duplicated motif [EHP (external hydrophobic patch)/IHP (internal hydrophobic patch)] regulating the assembly of mouse ZP proteins. Whereas the transmembrane domain (TMD) of ZP3 can be functionally replaced by an unrelated TMD, mutations in either EHP or IHP do not hinder secretion of full-length ZP3 but completely abolish its assembly. Because mutants truncated before the TMD are not processed, we conclude that the conserved TMD of mammalian ZP proteins does not engage them in specific interactions but is essential for C-terminal processing. Cleavage of ZP precursors results in loss of the EHP, thereby activating secreted polypeptides to assemble by using the IHP within the ZP domain. Taken together, these findings suggest a general mechanism for assembly of ZP domain proteins.
#7: Journal: Annu Rev Biochem / Year: 2005
Title: Zona pellucida domain proteins.
Authors: Luca Jovine / Costel C Darie / Eveline S Litscher / Paul M Wassarman /
Abstract: Many eukaryotic proteins share a sequence designated as the zona pellucida (ZP) domain. This structural element, present in extracellular proteins from a wide variety of organisms, from nematodes to ...Many eukaryotic proteins share a sequence designated as the zona pellucida (ZP) domain. This structural element, present in extracellular proteins from a wide variety of organisms, from nematodes to mammals, consists of approximately 260 amino acids with eight conserved cysteine (Cys) residues and is located close to the C terminus of the polypeptide. ZP domain proteins are often glycosylated, modular structures consisting of multiple types of domains. Predictions can be made about some of the structural features of the ZP domain and ZP domain proteins. The functions of ZP domain proteins vary tremendously, from serving as structural components of egg coats, appendicularian mucous houses, and nematode dauer larvae, to serving as mechanotransducers in flies and receptors in mammals and nonmammals. Generally, ZP domain proteins are present in filaments and/or matrices, which is consistent with the role of the domain in protein polymerization. A general mechanism for assembly of ZP domain proteins has been presented. It is likely that the ZP domain plays a common role despite its presence in proteins of widely diverse functions.
#8: Journal: Nature / Year: 2008
Title: Crystal Structure of the Zp-N Domain of Zp3 Reveals the Core Fold of Animal Egg Coats
Authors: Monne, M. / Han, L. / Schwend, T. / Burendahl, S. / Jovine, L.
History
DepositionJun 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zona pellucida 3
B: Zona pellucida 3
C: Zona pellucida 3
D: Zona pellucida 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1796
Polymers71,6064
Non-polymers5722
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.385, 98.385, 257.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28
19
29

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resid 54:71 and backbone
211chain B and resid 54:71 and backbone
112chain A and resid 77:96 and backbone
212chain B and resid 77:96 and backbone
113chain A and resid 100:132 and backbone
213chain B and resid 100:132 and backbone
114chain A and resid 146:156 and backbone
214chain B and resid 146:156 and backbone
115chain A and resid 183:203 and backbone
215chain B and resid 183:203 and backbone
116chain A and resid 206:213 and backbone
216chain B and resid 206:213 and backbone
117chain A and resid 223:315 and backbone
217chain B and resid 223:315 and backbone
118chain A and resid 321:340 and backbone
218chain B and resid 321:340 and backbone
119chain C and resid 368:379 and backbone
219chain D and resid 368:379 and backbone

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
DetailsCHAINS A AND B WERE CLEAVED IN TWO CHAINS GENERATING CHAINS C AND D, RESPECTIVELY. CHAINS A AND C; CHAINS B AND D BELONG TO THE SAME PROTEIN SEQUENCE.FOR ASSEMBLY DESCRIPTION OF THE BIOLOGICAL UNIT SEE REMARK 350

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Components

#1: Protein Zona pellucida 3 /


Mass: 32673.688 Da / Num. of mol.: 2 / Fragment: unp residues 21-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pDEF38/pNEF38 / Cell line (production host): DG44 CELLS / Production host: Chinese hamster (Chinese hamster) / References: UniProt: P79762
#2: Protein/peptide Zona pellucida 3 /


Mass: 3129.465 Da / Num. of mol.: 2 / Fragment: unp residues 359-382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pDEF38/pNEF38 / Cell line (production host): DG44 CELLS / Production host: Chinese hamster (Chinese hamster) / References: UniProt: P79762
#3: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen / Thomsen–Friedenreich antigen


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Thomsen-Friedenreich antigen
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAINS A AND B WERE CLEAVED IN TWO CHAINS BY TREATMENT WITH TRYPSIN BEFORE CRYSTALLIZATION ...CHAINS A AND B WERE CLEAVED IN TWO CHAINS BY TREATMENT WITH TRYPSIN BEFORE CRYSTALLIZATION EXPERIMENTS. CHAINS C AND D WERE GENERATED AS RESULT OF CLEAVAGE FROM CHAINS A AND B, RESPECTIVELY

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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: 4.35 Å3/Da / Density % sol: 71.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25 MG/ML PROTEIN IN 0.1 M SODIUM, CITRATE, 0.01 M TRIS-HCL, 4% PEG6000, 0.05 M SODIUM CHLORIDE, SAMPLE TO RESERVOIR RATIO IN DROP: 1:1 (DROP), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2007
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.6→61.2 Å / Num. obs: 37990 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 10.8
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2 / % possible all: 89.5

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D4G: PDB ENTRY 3D4G: RESIDUES 372-449 + 459-473
Resolution: 2.6→48.318 Å / SU ML: 0.45 / σ(F): 0 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 1903 5.03 %RANDOM
Rwork0.2187 ---
obs0.2202 37806 94.85 %-
all-39868 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.603 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.0093 Å20 Å2-0 Å2
2--10.0093 Å2-0 Å2
3----20.0185 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 38 127 4695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114689
X-RAY DIFFRACTIONf_angle_d1.1236400
X-RAY DIFFRACTIONf_dihedral_angle_d16.5921694
X-RAY DIFFRACTIONf_chiral_restr0.062742
X-RAY DIFFRACTIONf_plane_restr0.007849
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A72X-RAY DIFFRACTIONPOSITIONAL
12B72X-RAY DIFFRACTIONPOSITIONAL0.07
21A80X-RAY DIFFRACTIONPOSITIONAL
22B80X-RAY DIFFRACTIONPOSITIONAL0.071
31A132X-RAY DIFFRACTIONPOSITIONAL
32B132X-RAY DIFFRACTIONPOSITIONAL0.07
41A44X-RAY DIFFRACTIONPOSITIONAL
42B44X-RAY DIFFRACTIONPOSITIONAL0.071
51A84X-RAY DIFFRACTIONPOSITIONAL
52B84X-RAY DIFFRACTIONPOSITIONAL0.068
61A32X-RAY DIFFRACTIONPOSITIONAL
62B32X-RAY DIFFRACTIONPOSITIONAL0.044
71A372X-RAY DIFFRACTIONPOSITIONAL
72B372X-RAY DIFFRACTIONPOSITIONAL0.071
81A80X-RAY DIFFRACTIONPOSITIONAL
82B80X-RAY DIFFRACTIONPOSITIONAL0.04
91C48X-RAY DIFFRACTIONPOSITIONAL
92D48X-RAY DIFFRACTIONPOSITIONAL0.112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.73710.36122380.31484680X-RAY DIFFRACTION88
2.7371-2.90860.34132510.29734778X-RAY DIFFRACTION90
2.9086-3.13310.32632600.27214940X-RAY DIFFRACTION93
3.1331-3.44830.27442710.22615115X-RAY DIFFRACTION96
3.4483-3.94710.22512940.18815276X-RAY DIFFRACTION98
3.9471-4.97220.17352890.15025400X-RAY DIFFRACTION99
4.9722-48.3260.24033000.21155714X-RAY DIFFRACTION100
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)
13.0590.06561.96552.3783-0.04051.93720.07860.1-0.0304-0.1469-0.16720.0768-0.0240.103200.1685-0.01670.00040.2652-0.00240.307563.01281.755105.2256
24.1346-0.052-0.95371.13810.36593.3495-0.0083-0.67370.05560.1782-0.03340.1038-0.14060.02480.00010.1784-0.0032-0.01820.3469-0.05180.23834.698581.3767111.4579
31.59150.48950.51091.13950.11671.7630.05080.12380.0198-0.0011-0.1316-0.01610.13920.2591-00.22980.0161-0.01760.2986-0.00570.371437.952379.738470.9822
44.20190.13590.46253.7374-0.2122.5215-0.12420.63280.243-0.41530.0828-0.2992-0.55210.6747-00.3468-0.1584-0.01370.67620.13580.261966.321286.928166.7129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 51:157
2X-RAY DIFFRACTION2CHAIN A OR CHAIN C AND (RESID 167:343 OR RESID 368:388)
3X-RAY DIFFRACTION3CHAIN B AND RESID 52:157
4X-RAY DIFFRACTION4CHAIN B OR CHAIN D AND (RESID 180:343 OR RESID 368:381)

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