[English] 日本語
Yorodumi
- PDB-3u4e: Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u4e
TitleCrystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain CAP45
Components
  • PG9 Heavy Chain
  • PG9 Light Chain
  • V1V2 region of HIV-1 on 1FD6 scaffold
KeywordsIMMUNE SYSTEM / NEUTRALIZING ANTIBODIES / LONG CDRH3 / HIV-1
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Ubiquitin-like (UB roll) - #10 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Ubiquitin-like (UB roll) / Roll / Immunoglobulins ...Ubiquitin-like (UB roll) - #10 / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Ubiquitin-like (UB roll) / Roll / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.185 Å
AuthorsGorman, J. / McLellan, J. / Pancera, M. / Kwong, P.D.
CitationJournal: Nature / Year: 2011
Title: Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.
Authors: McLellan, J.S. / Pancera, M. / Carrico, C. / Gorman, J. / Julien, J.P. / Khayat, R. / Louder, R. / Pejchal, R. / Sastry, M. / Dai, K. / O'Dell, S. / Patel, N. / Shahzad-Ul-Hussan, S. / Yang, ...Authors: McLellan, J.S. / Pancera, M. / Carrico, C. / Gorman, J. / Julien, J.P. / Khayat, R. / Louder, R. / Pejchal, R. / Sastry, M. / Dai, K. / O'Dell, S. / Patel, N. / Shahzad-Ul-Hussan, S. / Yang, Y. / Zhang, B. / Zhou, T. / Zhu, J. / Boyington, J.C. / Chuang, G.Y. / Diwanji, D. / Georgiev, I. / Do Kwon, Y. / Lee, D. / Louder, M.K. / Moquin, S. / Schmidt, S.D. / Yang, Z.Y. / Bonsignori, M. / Crump, J.A. / Kapiga, S.H. / Sam, N.E. / Haynes, B.F. / Burton, D.R. / Koff, W.C. / Walker, L.M. / Phogat, S. / Wyatt, R. / Orwenyo, J. / Wang, L.X. / Arthos, J. / Bewley, C.A. / Mascola, J.R. / Nabel, G.J. / Schief, W.R. / Ward, A.B. / Wilson, I.A. / Kwong, P.D.
History
DepositionOct 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 2.0Dec 25, 2019Group: Advisory / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 3.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: V1V2 region of HIV-1 on 1FD6 scaffold
J: V1V2 region of HIV-1 on 1FD6 scaffold
H: PG9 Heavy Chain
L: PG9 Light Chain
A: PG9 Heavy Chain
B: PG9 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,96823
Polymers127,5056
Non-polymers5,46317
Water8,755486
1
G: V1V2 region of HIV-1 on 1FD6 scaffold
H: PG9 Heavy Chain
L: PG9 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,82913
Polymers63,7533
Non-polymers3,07710
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
J: V1V2 region of HIV-1 on 1FD6 scaffold
A: PG9 Heavy Chain
B: PG9 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,13910
Polymers63,7533
Non-polymers2,3867
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.026, 103.545, 186.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules GJ

#1: Protein V1V2 region of HIV-1 on 1FD6 scaffold


Mass: 13722.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Plasmid: PVRC8400 / Production host: Homo Sapiens (human) / References: UniProt: Q1PHM9*PLUS

-
Antibody , 2 types, 4 molecules HALB

#2: Antibody PG9 Heavy Chain


Mass: 27193.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PVRC8400 / Cell line (production host): HEK 293f / Production host: Homo sapiens (human)
#3: Antibody PG9 Light Chain


Mass: 22837.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PVRC8400 / Cell line (production host): HEK 293S GnTI- / Production host: Homo Sapiens (human)

-
Sugars , 4 types, 5 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: 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
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+1)][a-D-Manp]{}}LINUCSPDB-CARE

-
Non-polymers , 2 types, 498 molecules

#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 13% (w/v) PEG 3350, 11% (v/v) 2-methyl-2,4-pentanediol, 0.2 M lithium sulfate, 0.1 M imidazole pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2011
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 73822 / Num. obs: 67917 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 4.1 %
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.19-2.242.40.3392.4168.7
2.24-2.32.70.342.6173.4
2.3-2.362.90.342.7177.5
2.36-2.4330.3222.4182.1
2.43-2.513.20.3322.4187.1
2.51-2.63.30.3072.1193.1
2.6-2.73.70.3212.3198.1
2.7-2.824.30.2912.3199.9
2.82-2.974.90.2493.91100
2.97-3.1650.1944.51100
3.16-3.450.13710.51100
3.4-3.7450.106121100
3.74-4.2950.09213.81100
4.29-5.450.08214.41100
5.4-504.70.05418.7199

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U2S

3u2s


Resolution: 2.185→27.693 Å / SU ML: 0.71 / σ(F): 1.91 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 3442 5.09 %Random
Rwork0.1818 ---
obs0.1845 67657 91.49 %-
all-73950 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.7 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8889 Å2-0 Å20 Å2
2---6.6663 Å2-0 Å2
3---0.7774 Å2
Refinement stepCycle: LAST / Resolution: 2.185→27.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8478 0 348 486 9312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099040
X-RAY DIFFRACTIONf_angle_d1.09412297
X-RAY DIFFRACTIONf_dihedral_angle_d14.1623254
X-RAY DIFFRACTIONf_chiral_restr0.0761425
X-RAY DIFFRACTIONf_plane_restr0.0051517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1851-2.2150.3096870.23051655X-RAY DIFFRACTION59
2.215-2.24660.31991020.21451960X-RAY DIFFRACTION71
2.2466-2.28010.2507900.21922048X-RAY DIFFRACTION74
2.2801-2.31570.29711070.21972102X-RAY DIFFRACTION76
2.3157-2.35370.30941070.22512201X-RAY DIFFRACTION78
2.3537-2.39430.33731170.222219X-RAY DIFFRACTION81
2.3943-2.43780.29831220.22632324X-RAY DIFFRACTION83
2.4378-2.48460.32721230.23442427X-RAY DIFFRACTION87
2.4846-2.53530.29481390.24192503X-RAY DIFFRACTION90
2.5353-2.59040.29381430.25452590X-RAY DIFFRACTION94
2.5904-2.65060.26841430.24212683X-RAY DIFFRACTION97
2.6506-2.71680.30341340.23412776X-RAY DIFFRACTION99
2.7168-2.79020.32711480.23312759X-RAY DIFFRACTION99
2.7902-2.87230.28141740.21072755X-RAY DIFFRACTION100
2.8723-2.96490.29261660.20092779X-RAY DIFFRACTION100
2.9649-3.07070.26781540.19612765X-RAY DIFFRACTION99
3.0707-3.19350.26531440.19192801X-RAY DIFFRACTION100
3.1935-3.33860.24471430.1862838X-RAY DIFFRACTION100
3.3386-3.51430.23581560.17872806X-RAY DIFFRACTION100
3.5143-3.7340.19981490.16782813X-RAY DIFFRACTION100
3.734-4.02150.2051550.15362823X-RAY DIFFRACTION100
4.0215-4.42470.17521520.13492831X-RAY DIFFRACTION100
4.4247-5.06160.16351640.12352859X-RAY DIFFRACTION100
5.0616-6.36430.19231500.16012901X-RAY DIFFRACTION100
6.3643-27.69490.21341730.18832997X-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)
10.98790.6039-0.23021.2306-0.8293.0382-0.2318-0.0773-0.05440.20630.0305-0.30920.1773-0.0491-0.00370.27060.0360.07020.33460.04520.11632.43663.1945-52.0311
22.1511-1.24750.28752.1069-0.7881.3168-0.1039-0.0840.13290.07380.0659-0.08630.0322-0.0480.01280.2435-0.00330.02370.38650.07090.276726.227916.8322-59.3482
31.378-0.27510.27582.0566-0.83772.8649-0.3696-0.24610.1418-0.25560.0716-0.1963-0.16910.0913-0.01010.324-0.0132-0.06650.3237-0.01680.1961-3.934-2.074830.063
42.44061.2938-0.87552.0572-0.81191.6731-0.189-0.3622-0.2734-0.08680.00120.05350.0224-0.07240.01440.36330.00170.02590.48890.03240.354-11.0251-16.64136.8024
50.4329-0.00520.33250.6616-0.08591.6546-0.07810.0330.12330.00120.0231-0.2177-0.1589-0.0790.00820.1857-0.0274-0.04430.1537-0.00320.249434.27975.172-9.7873
61.0296-0.01360.08471.9629-0.93141.73460.03170.1104-0.0104-0.11110.0218-0.03970.0436-0.01790.01050.1594-0.01470.02440.1725-0.00230.110626.8926-9.2622-24.3788
71.4797-0.0265-0.08411.52410.26332.4230.0146-0.2241-0.0240.055-0.0241-0.0316-0.09290.1504-0.00090.1834-0.00080.00420.2292-0.0070.217133.9546-23.10514.6357
80.62030.3721-0.22332.0331-0.55821.5120.1076-0.04280.02390.0624-0.0348-0.1013-0.0641-0.0449-0.02410.1464-0.0014-0.02650.1611-0.00620.2168-9.098511.65653.4673
91.4623-0.06560.06911.50580.26222.31720.25410.3929-0.0302-0.0877-0.17920.3177-0.4051-0.0048-0.0330.48160.14130.0160.43370.02310.3838-0.457728.3794-36.1017
100.60720.2258-0.37570.7278-0.24121.36610.00110.087-0.0764-0.10240.0302-0.17280.1359-0.0525-0.02140.22210.0020.03110.167-0.00340.3288-2.4236-2.2375-12.2117
111.62760.40560.01783.0157-0.31461.4928-0.11270.07570.31830.29060.1223-0.0904-0.21370.0931-0.01210.35570.0255-0.01280.30040.0410.373211.559918.2773-30.2527
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resseq 1:180)
2X-RAY DIFFRACTION2chain 'G' and (resseq 190:244)
3X-RAY DIFFRACTION3chain 'J' and (resseq 1:180)
4X-RAY DIFFRACTION4chain 'J' and (resseq 190:245)
5X-RAY DIFFRACTION5chain 'L' and (resseq 1:116)
6X-RAY DIFFRACTION6chain 'H' and (resseq 1:113)
7X-RAY DIFFRACTION7chain 'H' and (resseq 114:216)
8X-RAY DIFFRACTION8chain 'A' and (resseq 1:113)
9X-RAY DIFFRACTION9chain 'A' and (resseq 114:216)
10X-RAY DIFFRACTION10chain 'B' and (resseq 2:116)
11X-RAY DIFFRACTION11chain 'B' and (resseq 117:209)

+
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