[English] 日本語
Yorodumi
- PDB-4irl: X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4irl
TitleX-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein
ComponentsMaltose-binding periplasmic protein, Novel protein similar to vertebrate guanylate binding protein family
KeywordsAPOPTOSIS / CARD / death fold superfamily / six-helix bundle / inflammasome / innate immune system / signal transduction
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / regulation of apoptotic process / periplasmic space / inflammatory response / innate immune response / GTPase activity / DNA damage response / GTP binding / membrane / cytosol
Similarity search - Function
FIIND domain / Function to find / UPA-FIIND domain / FIIND domain profile. / Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / CARD8/ASC/NALP1, CARD domain / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal ...FIIND domain / Function to find / UPA-FIIND domain / FIIND domain profile. / Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / CARD8/ASC/NALP1, CARD domain / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / Death Domain, Fas / Death Domain, Fas / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Death-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
alpha-maltotetraose / ACETATE ION / MALONATE ION / DI(HYDROXYETHYL)ETHER / Guanylate-binding protein 3 / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Danio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsJin, T. / Huang, M. / Smith, P. / Xiao, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of the caspase-recruitment domain from a zebrafish guanylate-binding protein.
Authors: Jin, T. / Huang, M. / Smith, P. / Jiang, J. / Xiao, T.S.
History
DepositionJan 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Nov 26, 2014Group: Refinement description
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose-binding periplasmic protein, Novel protein similar to vertebrate guanylate binding protein family
B: Maltose-binding periplasmic protein, Novel protein similar to vertebrate guanylate binding protein family
C: Maltose-binding periplasmic protein, Novel protein similar to vertebrate guanylate binding protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,94622
Polymers156,9543
Non-polymers2,99119
Water34,6251922
1
A: Maltose-binding periplasmic protein, Novel protein similar to vertebrate guanylate binding protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2316
Polymers52,3181
Non-polymers9135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein, Novel protein similar to vertebrate guanylate binding protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3789
Polymers52,3181
Non-polymers1,0608
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Maltose-binding periplasmic protein, Novel protein similar to vertebrate guanylate binding protein family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3377
Polymers52,3181
Non-polymers1,0196
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.749, 124.750, 178.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Maltose-binding periplasmic protein, Novel protein similar to vertebrate guanylate binding protein family / MBP / MMBP / Maltodextrin-binding protein / Uncharacterized protein


Mass: 52318.109 Da / Num. of mol.: 3 / Fragment: Zebrafish GBP-NLRP1 CARD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Danio rerio (zebrafish)
Strain: K12
Gene: b4034, GBP-NLRP1, JW3994, malE, CH211-195H23.5-001, gbp3
Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0AEX9, UniProt: B0V1H4
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE

-
Non-polymers , 6 types, 1938 molecules

#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1922 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG1000, 0.2 M Sodium Malonate, 0.1 M MES 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.447→50 Å / Num. all: 260018 / Num. obs: 243247 / % possible obs: 93.55 % / Observed criterion σ(I): 1.5 / Redundancy: 12.9 % / Biso Wilson estimate: 14.2 Å2 / Net I/σ(I): 8.17

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_1217)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→29.434 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 11928 5.02 %
Rwork0.1881 --
obs0.1899 237398 95.62 %
all-260018 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→29.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10716 0 199 1922 12837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111321
X-RAY DIFFRACTIONf_angle_d1.29415391
X-RAY DIFFRACTIONf_dihedral_angle_d13.1074153
X-RAY DIFFRACTIONf_chiral_restr0.0851727
X-RAY DIFFRACTIONf_plane_restr0.0061978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.48670.31452860.27385285X-RAY DIFFRACTION68
1.4867-1.50420.30033140.26875621X-RAY DIFFRACTION73
1.5042-1.52250.30542750.26095968X-RAY DIFFRACTION76
1.5225-1.54180.28083140.26326312X-RAY DIFFRACTION81
1.5418-1.56210.30893500.25126691X-RAY DIFFRACTION86
1.5621-1.58350.29813660.23487097X-RAY DIFFRACTION91
1.5835-1.60610.25593990.23887476X-RAY DIFFRACTION96
1.6061-1.63010.27474050.22637654X-RAY DIFFRACTION99
1.6301-1.65560.26813690.21917820X-RAY DIFFRACTION100
1.6556-1.68270.25144070.2097845X-RAY DIFFRACTION100
1.6827-1.71170.26214240.20327769X-RAY DIFFRACTION100
1.7117-1.74280.24813970.20187820X-RAY DIFFRACTION100
1.7428-1.77640.23654310.20227841X-RAY DIFFRACTION100
1.7764-1.81260.2314210.2047781X-RAY DIFFRACTION100
1.8126-1.8520.23564210.27771X-RAY DIFFRACTION100
1.852-1.89510.25243940.19747878X-RAY DIFFRACTION100
1.8951-1.94250.24264230.20147822X-RAY DIFFRACTION100
1.9425-1.9950.23834320.20287831X-RAY DIFFRACTION100
1.995-2.05370.23164210.19517828X-RAY DIFFRACTION100
2.0537-2.11990.22594230.19697846X-RAY DIFFRACTION100
2.1199-2.19570.23824240.19027835X-RAY DIFFRACTION100
2.1957-2.28360.23494260.19097850X-RAY DIFFRACTION100
2.2836-2.38740.22064460.18647839X-RAY DIFFRACTION100
2.3874-2.51330.22274060.19047906X-RAY DIFFRACTION100
2.5133-2.67060.23994200.19157892X-RAY DIFFRACTION100
2.6706-2.87670.23284390.18417946X-RAY DIFFRACTION100
2.8767-3.16580.21124260.17957895X-RAY DIFFRACTION100
3.1658-3.62320.19923920.16278027X-RAY DIFFRACTION100
3.6232-4.56220.17034400.14458027X-RAY DIFFRACTION100
4.5622-29.43940.18064370.16738297X-RAY DIFFRACTION99
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)
12.3840.0586-0.09672.96590.60282.4584-0.06490.11560.0662-0.25590.0515-0.0238-0.105-0.11690.00560.15360.00490.00630.07360.02550.0856-26.823138.8060.7158
22.9993-1.33060.1322.31180.26722.1146-0.0374-0.0134-0.1457-0.0641-0.01490.21260.05-0.15940.0440.12210.01420.00760.0841-0.01980.0867-36.458431.946912.5383
30.85120.1076-0.38620.50760.16960.77060.0665-0.1610.06110.0558-0.0159-0.0294-0.02710.0868-0.05510.14440.0314-0.01050.12350.00190.0942-25.911447.410933.3556
40.73150.38510.35340.55540.5871.3367-0.0005-0.0531-0.01620.0036-0.0056-0.01990.03080.01140.00550.11980.0499-0.0110.08040.00660.0881-22.98339.559420.4635
51.68221.41230.38482.22840.7083.3609-0.0677-0.1173-0.14470.01870.0569-0.35850.13410.32420.01410.11470.05650.00730.1285-0.01340.1383-16.770530.623313.8302
62.4922-0.0312-0.28010.65630.83571.21510.066-0.0061-0.0617-0.0372-0.07490.0911-0.0884-0.01980.01030.1250.01750.01990.08610.03150.0514-32.999242.998728.1882
76.78756.31746.43476.16946.11676.15380.0841-0.20690.147-0.0093-0.22550.215-0.0621-0.32170.19270.12840.03770.01040.1401-0.01660.1206-49.049644.303429.2798
83.365-0.0349-0.84723.955-1.31353.712-0.03590.05860.2849-0.3839-0.0689-0.2761-0.35980.05360.08980.2640.012-0.01870.1125-0.02850.1379-58.778747.46229.2244
94.60080.3380.05310.69141.57584.497-0.0835-0.3841-0.13260.0137-0.0035-0.00470.1628-0.05670.07690.19440.0604-0.01490.09120.01040.1352-59.712542.152216.7342
102.1407-0.3316-0.62823.6621.35612.5877-0.08390.12410.1203-0.20190.0792-0.0234-0.1112-0.0507-0.0280.14960.0207-0.0130.07950.00140.0917-25.8641-2.54740.0628
110.37010.26140.16950.380.16140.7563-0.0185-0.0084-0.00250.0345-0.00770.03190.13460.03420.02070.17660.0839-0.01070.1102-0.02540.1184-29.7829-6.345816.6808
122.78891.8992-0.45034.2576-0.0371.93310.1674-0.1580.0520.0156-0.1373-0.2201-0.2132-0.0167-0.02840.11670.0570.01160.1042-0.02190.0953-20.57711.157534.7895
133.87031.5161-0.63680.7944-0.39731.26460.0375-0.1603-0.1423-0.0689-0.1309-0.0534-0.0267-0.11940.08020.14360.0888-0.02450.1141-0.01290.1076-31.32016.6933.1833
140.45710.33170.43040.28740.29960.87560.0187-0.0223-0.04610.0124-0.0144-0.04160.02660.007-0.00980.12780.0671-0.01550.1057-0.00680.0961-21.7075-1.189620.1984
150.64820.52850.5460.55390.14681.1496-0.1032-0.1065-0.08550.10610.1178-0.2530.20810.33480.02360.22410.1501-0.04780.2242-0.06580.186-15.4564-10.490113.6491
161.72150.79920.69820.39330.4210.73450.037-0.12410.05-0.0497-0.11260.1155-0.0367-0.09530.07010.1740.0807-0.02420.1616-0.02120.1061-37.0163.071428.1495
172.45751.0015-0.78655.0357-1.41254.1830.00710.02710.2966-0.07790.0267-0.1216-0.10190.0671-0.0390.1060.0337-0.01170.0722-0.02730.1445-57.67766.44967.9717
183.93150.3605-0.05130.98841.64193.2574-0.0927-0.4369-0.05470.14310.0623-0.02410.20250.07180.03140.15340.0508-0.02580.07870.00050.1394-58.56610.964216.2996
191.4912-0.6379-0.44543.11111.26771.4786-0.0720.03630.1356-0.3301-0.020.0902-0.3348-0.10570.05050.21790.0237-0.02050.0767-0.00730.108-25.4904-44.3820.6899
202.1289-0.90750.09892.32880.52631.2922-0.1003-0.2239-0.0105-0.0187-0.00020.1887-0.0808-0.26470.07590.13480.0396-0.0070.1525-0.03370.099-35.0468-50.80712.7455
210.22760.44890.12211.88891.50311.6092-0.0251-0.1748-0.0042-0.06990.0118-0.1253-0.1365-0.10670.0120.11350.0524-0.00040.1439-0.00030.093-15.2043-40.396829.4832
221.51690.39950.1862.13920.77651.24280.24340.03520.1019-0.172-0.2034-0.1252-0.2846-0.251-0.04120.16280.07960.00810.2336-0.03950.0802-20.7049-30.153834.7472
231.28490.05310.32680.62220.57991.28150.2331-0.0626-0.169-0.1497-0.3620.0989-0.0028-0.49550.12250.20650.1525-0.02480.2834-0.10570.1596-31.2465-34.399733.2056
240.18570.28040.40920.61490.81521.3218-0.0109-0.0705-0.0228-0.0252-0.0008-0.03540.0218-0.06020.02110.12670.05740.00140.1289-0.00890.0903-21.6633-42.776720.3457
251.55221.79081.3752.36031.8093.6244-0.014-0.1571-0.15770.0760.0876-0.23160.16220.2277-0.05270.11070.06060.01410.1407-0.01090.1275-15.491-51.984314.2763
260.29260.042-0.17850.48750.14240.1581-0.0774-0.25850.0597-0.026-0.11790.0936-0.1076-0.3293-0.01140.19960.1633-0.050.4221-0.16060.1551-37.0203-38.588628.2223
271.00180.1543-0.07474.0153-1.30854.92390.0101-0.15040.3721-0.1879-0.0279-0.3441-0.24320.12480.01210.1040.02880.03060.1177-0.06590.255-57.4444-35.01768.3844
284.25910.3329-0.26920.79971.51093.116-0.1245-0.66630.06270.18660.1004-0.12210.28850.19050.0140.16490.0724-0.03440.1889-0.05170.1646-58.797-40.477316.656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 219 )
4X-RAY DIFFRACTION4chain 'A' and (resid 220 through 283 )
5X-RAY DIFFRACTION5chain 'A' and (resid 284 through 315 )
6X-RAY DIFFRACTION6chain 'A' and (resid 316 through 357 )
7X-RAY DIFFRACTION7chain 'A' and (resid 358 through 381 )
8X-RAY DIFFRACTION8chain 'A' and (resid 382 through 419 )
9X-RAY DIFFRACTION9chain 'A' and (resid 420 through 462 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 43 )
11X-RAY DIFFRACTION11chain 'B' and (resid 44 through 129 )
12X-RAY DIFFRACTION12chain 'B' and (resid 130 through 164 )
13X-RAY DIFFRACTION13chain 'B' and (resid 165 through 219 )
14X-RAY DIFFRACTION14chain 'B' and (resid 220 through 283 )
15X-RAY DIFFRACTION15chain 'B' and (resid 284 through 315 )
16X-RAY DIFFRACTION16chain 'B' and (resid 316 through 381 )
17X-RAY DIFFRACTION17chain 'B' and (resid 382 through 419 )
18X-RAY DIFFRACTION18chain 'B' and (resid 420 through 463 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 43 )
20X-RAY DIFFRACTION20chain 'C' and (resid 44 through 106 )
21X-RAY DIFFRACTION21chain 'C' and (resid 107 through 129 )
22X-RAY DIFFRACTION22chain 'C' and (resid 130 through 164 )
23X-RAY DIFFRACTION23chain 'C' and (resid 165 through 219 )
24X-RAY DIFFRACTION24chain 'C' and (resid 220 through 283 )
25X-RAY DIFFRACTION25chain 'C' and (resid 284 through 315 )
26X-RAY DIFFRACTION26chain 'C' and (resid 316 through 381 )
27X-RAY DIFFRACTION27chain 'C' and (resid 382 through 419 )
28X-RAY DIFFRACTION28chain 'C' and (resid 420 through 462 )

+
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