[English] 日本語
Yorodumi
- PDB-3hrz: Cobra Venom Factor (CVF) in complex with human factor B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hrz
TitleCobra Venom Factor (CVF) in complex with human factor B
Components
  • (Cobra venom factor) x 3
  • Complement factor B
KeywordsIMMUNE SYSTEM / serine protease / glycosilated / multi-domain / complement system / convertase / Complement alternate pathway / Complement pathway / Disulfide bond / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Secreted / Thioester bond / Cleavage on pair of basic residues / Glycation / Hydrolase / Protease / Sushi / Zymogen
Function / homology
Function and homology information


alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / endopeptidase inhibitor activity / Regulation of Complement cascade / response to bacterium ...alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / endopeptidase inhibitor activity / Regulation of Complement cascade / response to bacterium / toxin activity / blood microparticle / inflammatory response / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
ubp-family deubiquitinating enzyme fold - #20 / N-terminal domain of TfIIb - #160 / Complement factor B / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / Complement B/C2 / S-adenosyl-L-methionine-dependent methyltransferases / ubp-family deubiquitinating enzyme fold ...ubp-family deubiquitinating enzyme fold - #20 / N-terminal domain of TfIIb - #160 / Complement factor B / S-adenosyl-L-methionine-dependent methyltransferases - #20 / Immunoglobulin-like - #1940 / Alpha-macroglobulin, receptor-binding domain / Macroglobulin (MG2) domain / Complement B/C2 / S-adenosyl-L-methionine-dependent methyltransferases / ubp-family deubiquitinating enzyme fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / N-terminal domain of TfIIb / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Other non-globular / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / von Willebrand factor type A domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Single Sheet / von Willebrand factor A-like domain superfamily / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Immunoglobulins / Peptidase S1, PA clan / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Complement factor B / Cobra venom factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Naja kaouthia (monocled cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsJanssen, B.J.C. / Gomes, L. / Koning, R.I. / Svergun, D.I. / Koster, A.J. / Fritzinger, D.C. / Vogel, C.-W. / Gros, P.
CitationJournal: Embo J. / Year: 2009
Title: Insights into complement convertase formation based on the structure of the factor B-cobra venom factor complex
Authors: Janssen, B.J. / Gomes, L. / Koning, R.I. / Svergun, D.I. / Koster, A.J. / Fritzinger, D.C. / Vogel, C.W. / Gros, P.
History
DepositionJun 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / 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.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cobra venom factor
B: Cobra venom factor
C: Cobra venom factor
D: Complement factor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,03718
Polymers224,8224
Non-polymers2,21514
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24920 Å2
ΔGint-123 kcal/mol
Surface area81780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.890, 283.390, 134.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 4 types, 4 molecules ABCD

#1: Protein Cobra venom factor / CVF / Complement C3 homolog / Cobra venom factor alpha chain / Cobra venom factor gamma chain / ...CVF / Complement C3 homolog / Cobra venom factor alpha chain / Cobra venom factor gamma chain / Cobra venom factor beta chain


Mass: 69581.984 Da / Num. of mol.: 1 / Fragment: residues 23-649 / Source method: isolated from a natural source / Details: Cobra venom / Source: (natural) Naja kaouthia (monocled cobra) / References: UniProt: Q91132
#2: Protein Cobra venom factor / CVF / Complement C3 homolog / Cobra venom factor alpha chain / Cobra venom factor gamma chain / ...CVF / Complement C3 homolog / Cobra venom factor alpha chain / Cobra venom factor gamma chain / Cobra venom factor beta chain


Mass: 28418.568 Da / Num. of mol.: 1 / Fragment: residues 733-984 / Source method: isolated from a natural source / Details: Cobra venom / Source: (natural) Naja kaouthia (monocled cobra) / References: UniProt: Q91132
#3: Protein Cobra venom factor / CVF / Complement C3 homolog / Cobra venom factor alpha chain / Cobra venom factor gamma chain / ...CVF / Complement C3 homolog / Cobra venom factor alpha chain / Cobra venom factor gamma chain / Cobra venom factor beta chain


Mass: 43626.547 Da / Num. of mol.: 1 / Fragment: residues 1264-1642 / Source method: isolated from a natural source / Details: Cobra venom / Source: (natural) Naja kaouthia (monocled cobra) / References: UniProt: Q91132
#4: Protein Complement factor B / C3/C5 convertase / Properdin factor B / Glycine-rich beta glycoprotein / GBG / PBF2 / Complement ...C3/C5 convertase / Properdin factor B / Glycine-rich beta glycoprotein / GBG / PBF2 / Complement factor B Ba fragment / Complement factor B Bb fragment


Mass: 83194.859 Da / Num. of mol.: 1 / Fragment: residues 26-764 / Mutation: D279G,N285D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFB, BF, BFD / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: P00751, alternative-complement-pathway C3/C5 convertase

-
Sugars , 2 types, 4 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 5 types, 761 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#10: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 3350, PEG 400, Na/K Phosphate, Bis-Tris propane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9834 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9834 Å / Relative weight: 1
ReflectionResolution: 2.2→34 Å / Num. all: 124437 / Num. obs: 123939 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.6 / Num. measured all: 67190 / Num. unique all: 17889 / Rsym value: 0.602 / % possible all: 99.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OK5 and 2I07
Resolution: 2.2→33.487 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.846 / SU ML: 0.3 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2486 2.01 %random
Rwork0.18 ---
all0.181 124437 --
obs0.181 123930 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.48 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 142.3 Å2 / Biso mean: 44.995 Å2 / Biso min: 13.73 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15051 0 136 751 15938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715538
X-RAY DIFFRACTIONf_angle_d1.11321037
X-RAY DIFFRACTIONf_chiral_restr0.0692366
X-RAY DIFFRACTIONf_plane_restr0.0042684
X-RAY DIFFRACTIONf_dihedral_angle_d16.7035703
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2410.351400.2746625676598
2.241-2.2870.3091330.2526697683099
2.287-2.3370.2861560.2326646680299
2.337-2.3910.2691260.2216714684099
2.391-2.4510.2871450.2166640678599
2.451-2.5170.2431460.19967116857100
2.517-2.5910.2541250.1976708683399
2.591-2.6750.2661350.267156850100
2.675-2.770.2911280.20467266854100
2.77-2.8810.2541440.20267196863100
2.881-3.0120.2661300.19767516881100
3.012-3.1710.221410.20167716912100
3.171-3.370.2621430.18467506893100
3.37-3.6290.2231380.17467806918100
3.629-3.9940.1831330.15868226955100
3.994-4.5710.1671470.13668446991100
4.571-5.7540.1721300.13168737003100
5.754-33.4910.1841460.1556952709898
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)
11.43380.9274-0.28363.0338-0.85883.8302-0.04890.3093-0.0864-0.4918-0.1546-0.08790.0434-0.302-0.00040.47380.05270.01810.2443-0.02930.1975-21.846818.64819.2512
22.9157-0.7388-0.41123.0368-0.432.22960.09790.12310.0614-0.2304-0.0735-0.1358-0.12780.0643-0.00020.37340.00190.01560.1411-0.03440.1744-24.4273-16.812618.9354
32.64941.60381.58063.9761.87362.6039-0.14610.00360.0706-0.05580.0398-0.103-0.1879-0.00950.00020.32610.01680.01860.12130.01160.1625-25.7249-21.607751.9437
41.6922-0.1680.21072.5491-0.9993.35280.0301-0.11990.05330.3701-0.03170.067-0.1551-0.0249-0.00030.5680.0667-0.010.1641-0.02050.2121-25.179412.847149.6955
51.85960.8230.47282.89090.07732.02460.0242-0.00660.13520.1437-0.04240.2633-0.4233-0.1824-0.00020.5050.12340.00830.1489-0.03530.2018-31.345724.284430.0326
61.65950.7805-0.5782.74450.33471.50830.0133-0.010.2511-0.1637-0.05390.5638-0.3285-0.267-0.00020.36570.0797-0.03750.1867-0.05060.3084-46.8226-15.62424.1985
70.07660.48770.30641.49910.0848-0.0131-0.0282-0.0311-0.20490.0677-0.1325-0.3660.0266-0.00080.00060.48770.04450.0310.2066-0.00210.3088-22.22076.19427.7886
80.4898-0.52630.17550.07390.1943-0.0117-0.51470.3663-0.2351-0.16660.52450.68150.3645-0.73830.00120.4636-0.06740.04010.3550.01910.4903-52.3286-46.456229.0398
92.4108-0.5323-0.34211.97440.27381.85390.00910.0257-0.06960.15760.01030.16940.1392-0.2246-00.3747-0.02620.03960.184-0.02080.2337-41.1186-47.733734.3573
102.47790.1339-0.86281.3304-0.54853.5375-0.1527-0.0546-0.3207-0.1819-0.0153-0.10050.2219-0.0926-0.00070.375-0.00270.01450.25750.01590.4366-6.5894-33.2468.8212
112.73660.629-0.44833.22790.5862.40240.0036-0.1967-0.19120.2594-0.045-0.27560.45130.0641-0.00020.44880.0212-0.01450.1394-0.01250.212-28.5076-50.331652.5063
120.6325-1.14240.21220.65390.33720.6314-0.05710.4585-0.4911-0.2821-0.0234-0.0040.3432-0.1081-0.00090.6985-0.0340.02350.2038-0.09240.4004-27.7391-63.250531.1007
133.46680.07191.71794.299-0.1813.9797-0.0455-0.17180.03360.66150.1281-0.14120.17720.1618-0.00010.69870.046-0.0140.1451-0.04060.2228-34.4289-81.13718.3684
141.38930.1954-0.67511.8627-0.951.0893-0.0021-0.2272-0.8710.3336-0.2330.03480.69370.0443-0.00070.8768-0.06880.14480.5499-0.03950.9076-61.3756-63.800513.6533
152.84040.1488-1.07682.81691.02782.62570.0339-0.1431-0.05390.0237-0.22430.1991-0.1501-0.1914-0.00050.4129-0.0165-0.01720.2106-0.040.19-42.9122-38.46259.6221
162.3718-0.3032-0.36673.13040.10782.70380.21220.34930.1725-0.239-0.0431-0.1491-0.0993-0.05460.00020.4420.01540.04890.20250.01290.191-41.5895-60.4735-10.4939
173.154-0.4225-0.96271.1843-0.05692.87030.23810.29410.2403-0.3041-0.1766-0.2137-0.25430.2218-0.00020.56580.11490.09510.28670.08020.2534-75.9849-36.6759-12.8985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 1:101A1 - 101
2X-RAY DIFFRACTION2chain A and (resseq 102:199 or resseq 187:187)A102 - 199
3X-RAY DIFFRACTION2chain A and (resseq 102:199 or resseq 187:187)A187
4X-RAY DIFFRACTION3chain A and resseq 200:318A200 - 318
5X-RAY DIFFRACTION4chain A and resseq 319:412A319 - 412
6X-RAY DIFFRACTION5chain A and resseq 413:520A413 - 520
7X-RAY DIFFRACTION6(chain A or chain B) and (resseq 521:559 or resseq 729:789)A0
8X-RAY DIFFRACTION7chain A and resseq 560:627A560 - 627
9X-RAY DIFFRACTION8chain B and resseq 711:728B711 - 728
10X-RAY DIFFRACTION9chain B and resseq 790:896B790 - 896
11X-RAY DIFFRACTION10(chain B or chain C) and (resseq 897:946 or resseq 1251:1313)B0
12X-RAY DIFFRACTION11chain C and (resseq 1314:1452 or resseq 1324:1324)C1314 - 1452
13X-RAY DIFFRACTION11chain C and (resseq 1314:1452 or resseq 1324:1324)C1324
14X-RAY DIFFRACTION12chain C and resseq 1453:1475C1453 - 1475
15X-RAY DIFFRACTION13chain C and resseq 1476:1620C1476 - 1620
16X-RAY DIFFRACTION14chain D and resseq 1:75D1 - 75
17X-RAY DIFFRACTION15chain D and (resseq 76:199 or resseq 9097:9099 or resseq 9117:9118)D76 - 199
18X-RAY DIFFRACTION15chain D and (resseq 76:199 or resseq 9097:9099 or resseq 9117:9118)D9097 - 9099
19X-RAY DIFFRACTION15chain D and (resseq 76:199 or resseq 9097:9099 or resseq 9117:9118)D9117 - 9118
20X-RAY DIFFRACTION16chain D and (resseq 200:449 or resseq 9353:9353)D200 - 449
21X-RAY DIFFRACTION16chain D and (resseq 200:449 or resseq 9353:9353)D9353
22X-RAY DIFFRACTION17chain D and resseq 450:742D450 - 742

+
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