[English] 日本語
Yorodumi
- PDB-4fp8: Crystal structure of broadly neutralizing antibody C05 bound to H... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fp8
TitleCrystal structure of broadly neutralizing antibody C05 bound to H3 influenza hemagglutinin, HA1 subunit
Components
  • (Antibody C05, ...) x 2
  • Hemagglutinin HA1 chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / viral fusion protein / immunoglobulin / virus attachment and entry / immune recognition / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.947 Å
AuthorsEkiert, D.C. / Wilson, I.A.
CitationJournal: Nature / Year: 2012
Title: Cross-neutralization of influenza A viruses mediated by a single antibody loop.
Authors: Damian C Ekiert / Arun K Kashyap / John Steel / Adam Rubrum / Gira Bhabha / Reza Khayat / Jeong Hyun Lee / Michael A Dillon / Ryann E O'Neil / Aleksandr M Faynboym / Michael Horowitz / ...Authors: Damian C Ekiert / Arun K Kashyap / John Steel / Adam Rubrum / Gira Bhabha / Reza Khayat / Jeong Hyun Lee / Michael A Dillon / Ryann E O'Neil / Aleksandr M Faynboym / Michael Horowitz / Lawrence Horowitz / Andrew B Ward / Peter Palese / Richard Webby / Richard A Lerner / Ramesh R Bhatt / Ian A Wilson /
Abstract: Immune recognition of protein antigens relies on the combined interaction of multiple antibody loops, which provide a fairly large footprint and constrain the size and shape of protein surfaces that ...Immune recognition of protein antigens relies on the combined interaction of multiple antibody loops, which provide a fairly large footprint and constrain the size and shape of protein surfaces that can be targeted. Single protein loops can mediate extremely high-affinity binding, but it is unclear whether such a mechanism is available to antibodies. Here we report the isolation and characterization of an antibody called C05, which neutralizes strains from multiple subtypes of influenza A virus, including H1, H2 and H3. X-ray and electron microscopy structures show that C05 recognizes conserved elements of the receptor-binding site on the haemagglutinin surface glycoprotein. Recognition of the haemagglutinin receptor-binding site is dominated by a single heavy-chain complementarity-determining region 3 loop, with minor contacts from heavy-chain complementarity-determining region 1, and is sufficient to achieve nanomolar binding with a minimal footprint. Thus, binding predominantly with a single loop can allow antibodies to target small, conserved functional sites on otherwise hypervariable antigens.
History
DepositionJun 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Oct 10, 2012Group: Database references
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_conn_angle / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1May 19, 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 3.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA1 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA1 chain
H: Antibody C05, heavy chain
L: Antibody C05, light chain
I: Antibody C05, heavy chain
M: Antibody C05, light chain
J: Antibody C05, heavy chain
N: Antibody C05, light chain
K: Antibody C05, heavy chain
O: Antibody C05, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,68123
Polymers318,29112
Non-polymers1,39011
Water0
1
A: Hemagglutinin HA1 chain
H: Antibody C05, heavy chain
L: Antibody C05, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9907
Polymers79,5733
Non-polymers4174
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemagglutinin HA1 chain
I: Antibody C05, heavy chain
M: Antibody C05, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6384
Polymers79,5733
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hemagglutinin HA1 chain
J: Antibody C05, heavy chain
N: Antibody C05, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1937
Polymers79,5733
Non-polymers6214
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hemagglutinin HA1 chain
K: Antibody C05, heavy chain
O: Antibody C05, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8595
Polymers79,5733
Non-polymers2872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.794, 247.720, 95.380
Angle α, β, γ (deg.)90.00, 91.33, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Antibody , 2 types, 8 molecules HIJKLMNO

#2: Antibody
Antibody C05, heavy chain


Mass: 25474.379 Da / Num. of mol.: 4 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human)
#3: Antibody
Antibody C05, light chain


Mass: 23367.018 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 Freestyle / Production host: Homo sapiens (human)

-
Protein / Non-polymers , 2 types, 12 molecules ABCD

#1: Protein
Hemagglutinin HA1 chain / Hemagglutinin receptor binding subunit HA1


Mass: 30731.434 Da / Num. of mol.: 4 / Fragment: UNP residues 59-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

-
Sugars , 2 types, 3 molecules

#4: 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
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 10% w/v PEG3000, 200 mM zinc acetate, 100 mM sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.921→50 Å / Num. obs: 84287 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 69.9 Å2 / Rsym value: 0.1 / Net I/σ(I): 10.9
Reflection shellResolution: 2.921→3.06 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.58 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
Blu-IceEpicsdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4FNK AND 4FNL

4fnk

4fnl


Resolution: 2.947→44.495 Å / SU ML: 0.77 / σ(F): 0 / Phase error: 23.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.241 4191 4.98 %RANDOM
Rwork0.2122 ---
obs0.2136 84209 95.1 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.708 Å2 / ksol: 0.299 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6741 Å2-0 Å2-0.9601 Å2
2--0.111 Å20 Å2
3---2.5631 Å2
Refinement stepCycle: LAST / Resolution: 2.947→44.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21913 0 64 0 21977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522984
X-RAY DIFFRACTIONf_angle_d1.10431281
X-RAY DIFFRACTIONf_dihedral_angle_d13.7058340
X-RAY DIFFRACTIONf_chiral_restr0.0673482
X-RAY DIFFRACTIONf_plane_restr0.0064069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.947-2.980.38011230.33872435X-RAY DIFFRACTION87
2.98-3.0150.31681270.32082693X-RAY DIFFRACTION97
3.015-3.05180.35421590.30142730X-RAY DIFFRACTION97
3.0518-3.09040.34131460.2942710X-RAY DIFFRACTION97
3.0904-3.13110.28831500.2782698X-RAY DIFFRACTION97
3.1311-3.17390.27411500.27562739X-RAY DIFFRACTION97
3.1739-3.21930.28611310.26512645X-RAY DIFFRACTION96
3.2193-3.26730.2861340.27092758X-RAY DIFFRACTION97
3.2673-3.31840.33191450.26232674X-RAY DIFFRACTION97
3.3184-3.37270.28741290.25482726X-RAY DIFFRACTION96
3.3727-3.43090.28681440.24962709X-RAY DIFFRACTION97
3.4309-3.49320.24371280.23372730X-RAY DIFFRACTION96
3.4932-3.56040.24751510.23512650X-RAY DIFFRACTION96
3.5604-3.6330.28451350.23062731X-RAY DIFFRACTION96
3.633-3.7120.24611490.22992648X-RAY DIFFRACTION96
3.712-3.79830.25361580.22612701X-RAY DIFFRACTION96
3.7983-3.89320.2391170.21752662X-RAY DIFFRACTION96
3.8932-3.99840.22411490.20972714X-RAY DIFFRACTION96
3.9984-4.1160.24951420.18682654X-RAY DIFFRACTION95
4.116-4.24880.20261160.18672672X-RAY DIFFRACTION95
4.2488-4.40050.22441350.17922685X-RAY DIFFRACTION95
4.4005-4.57650.19531600.16622649X-RAY DIFFRACTION95
4.5765-4.78460.17751380.15512676X-RAY DIFFRACTION95
4.7846-5.03650.18281380.16252658X-RAY DIFFRACTION95
5.0365-5.35160.19381500.17332632X-RAY DIFFRACTION94
5.3516-5.7640.2481580.19042598X-RAY DIFFRACTION94
5.764-6.34250.25931560.2052626X-RAY DIFFRACTION93
6.3425-7.25690.23461110.21472638X-RAY DIFFRACTION93
7.2569-9.12990.21551270.18542619X-RAY DIFFRACTION92
9.1299-44.49960.21341350.19382558X-RAY DIFFRACTION90
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)
10.35541.08350.11564.0020.07271.97570.11680.321-0.977-0.63710.05780.12750.5131-0.0558-0.07340.7984-0.2264-0.21731.0613-0.43541.3884-116.4562-111.012831.357
21.88560.89691.61962.77240.04663.1461-0.13120.6511-0.1175-0.15630.12260.05280.05180.1310.10560.4804-0.0247-0.00330.4743-0.10240.727-98.2296-101.297940.9748
32.9037-0.70841.89880.1947-0.4341.2941-0.29440.0103-0.35530.04860.0750.25580.0006-0.336-0.01430.53810.02910.04090.4914-0.08070.6778-98.0386-105.353543.4344
42.6131-0.106-0.40672.5835-0.00480.9895-0.2663-0.1251-0.46130.18190.00910.35960.0534-0.1052-0.00380.46610.01080.08690.31980.08260.4982-96.8446-97.69354.6941
56.3995-0.1314-0.00534.9240.5253.354-0.17490.149-0.1870.1535-0.0447-0.3621-0.23020.2195-0.00280.3796-0.04660.01930.2890.01390.4474-83.6077-94.86953.076
66.744-0.903-0.94332.37850.24831.2015-0.3149-0.7977-0.30410.39640.17690.2317-0.1379-0.01010.07820.51910.09140.09930.3790.12320.3832-98.4504-97.262862.7042
71.47010.17060.87956.67260.11831.112-0.2698-0.4959-0.41060.39880.0033-0.86120.41570.65050.31110.47820.0333-0.10840.56270.23940.7071-75.5205-103.246861.652
83.0569-1.9592-0.39976.38731.61024.4981-0.4302-0.2399-0.93680.47190.23810.04020.3922-0.2150.62490.42950.022-0.02380.47120.15250.5691-87.4305-107.51160.0495
92.2393-0.2417-0.47072.7050.59281.95470.0785-0.3867-0.50480.27380.15970.12630.1034-0.25340.22410.45730.02860.06240.40330.18290.4386-97.0504-102.552562.5764
102.03960.3669-0.46992.80351.61333.1938-0.16730.2594-0.66280.0106-0.35220.6105-0.0456-0.4998-0.45370.41430.01710.06890.441-0.01470.5962-102.8291-102.95949.3118
115.6402-1.54720.26562.79291.19270.9658-0.59580.0254-0.1717-0.16050.4251.4640.2606-1.1150.09120.6676-0.2046-0.0681.2124-0.3371.5009-118.9452-113.483732.2799
120.51570.66020.50372.70841.07450.5912-0.00370.0191-0.4709-0.09580.0073-0.01380.3019-0.1992-0.04170.824-0.4410.15340.9325-0.36251.729-117.0172-120.211538.4751
136.9637-4.8738-0.5818.73640.04163.44590.01610.9784-0.4249-1.1720.1223-0.5745-0.02580.7788-0.03841.4669-0.05950.30321.7669-0.25420.985314.7858-49.798225.7545
144.59291.2205-0.33793.92411.23025.92270.24561.00870.1264-0.11370.2354-0.9001-0.16970.4649-0.59570.5233-0.10360.01720.78240.02480.62065.9361-39.694644.0541
152.01180.0711-0.43991.8060.12535.7671-0.37531.28080.2692-0.35410.3075-0.1491-0.160.39380.06320.4614-0.10960.03020.8343-0.00310.49693.235-43.601744.3345
164.3013-4.1372-2.13638.24464.81686.5106-0.01281.48070.4414-1.4181-0.3592-0.3747-0.40710.07430.38630.5843-0.1576-0.0690.8210.09970.4323-4.231-41.138938.4423
175.9218-2.7374-1.95075.05040.38084.84490.0026-0.00751.2734-0.20020.04860.1203-0.51490.1606-0.06820.5296-0.0354-0.07470.2368-0.0380.6103-7.6137-31.026657.5709
184.6828-0.8054-1.22533.3141-0.41197.6272-0.16670.3630.4064-0.46120.0640.6647-0.2994-0.48630.04340.4038-0.1038-0.12060.2758-0.01780.5831-14.9623-37.078653.7984
195.3234-0.7582-0.25233.8464-1.10954.39690.410.2944-0.6541-0.49470.17050.69450.2815-0.255-0.59950.4205-0.057-0.12660.3151-0.07940.5763-13.1581-44.894455.1573
203.7758-1.0719-0.51563.64850.44722.61930.01051.26470.1187-0.7244-0.07320.3211-0.19510.20070.02730.5311-0.0923-0.11940.6903-0.03110.4563-7.9999-40.512842.0735
212.9713-1.4098-2.11272.2255-0.72967.067-0.44181.1681-0.3429-1.09550.2146-0.17960.02520.39320.11451.33850.02240.28961.8527-0.41220.886713.7804-52.290723.2724
220.1699-0.1561-0.34010.42980.59610.9613-0.13610.2128-0.1581-0.62630.1982-0.13180.17050.1505-0.15111.70350.1454-0.14551.674-0.76530.91087.3284-58.857325.2584
239.7675-0.558-0.10220.0690.19630.98650.2589-0.74120.71670.54020.21021.71930.9552-1.0058-0.4481.0658-0.24510.38431.96420.04581.77332.5649-51.023589.8973
243.6075-0.6289-0.13182.502-0.6213.3785-0.1272-0.27260.14740.21330.2007-0.2865-0.10370.0043-0.0720.34770.0158-0.0420.385-0.0760.515926.2969-45.993266.1041
255.33050.49720.17823.8763-0.00782.0108-0.24-0.8832-0.23760.5570.1498-0.22820.1058-0.2960.09020.40570.092-0.05930.5771-0.03320.516427.1154-49.348674.4379
260.6061-0.13221.39450.0326-0.32083.29090.08660.1107-0.9292-0.3138-0.3611-0.45881.77670.40960.24012.30010.19090.60852.33620.15041.43682.4338-54.811492.2634
279.13186.72291.46864.94921.0810.2359-0.26470.2912-0.131-0.083-0.006-0.22940.3817-0.13380.36832.3231-0.6701-0.25592.46130.90991.96866.1867-62.512589.1084
280.754-0.8526-2.0841.0232.42345.8381-0.06790.1202-0.5871-0.7197-0.22320.24750.3178-0.50870.28891.40160.07710.13022.89350.2871.56-40.110410.642450.7833
292.92460.5485-1.2662.1558-1.12133.1540.11180.46760.21570.11840.23260.36-0.4372-0.6435-0.26320.45570.0740.10530.43470.10060.4905-17.196217.070175.0781
300.9276-0.0625-1.56723.09740.3622.74340.1010.92990.13240.07470.23780.648-0.0956-1.296-0.2250.48310.02410.07430.80730.18440.5504-25.410713.696475.6624
314.1199-1.9526-0.42541.19461.02482.5617-0.4366-0.176-0.56890.152-0.53260.31240.3688-0.57020.86081.9166-1.0707-0.52933.68940.04452.8134-42.18477.268450.564
320.0230.0019-0.00840-0.00080.00290.03410.6740.2609-0.87760.4509-1.1835-0.67591.1099-0.41453.2842-1.1958-0.07123.1632-0.46172.6737-39.1838-1.038354.8025
332.67870.6924-0.3015.0940.12230.1231-0.23150.4589-0.6594-0.17930.1121-0.04980.35350.37760.12050.5115-0.0103-0.11270.5834-0.15330.4725-56.2734-88.804145.921
342.35931.1634-0.74341.6765-0.39821.0987-0.17820.4610.384-0.35980.35160.38180.0980.10230.00480.4237-0.1056-0.07650.5490.01920.466-60.3699-82.008744.7057
356.0511-0.2686-2.44216.1812-4.07183.8187-0.1055-1.02510.27291.0966-0.04-0.9431-0.80741.49630.12990.4842-0.0416-0.00280.6161-0.17450.7328-19.3465-72.724459.3349
361.9633-0.37780.55293.407-1.09193.6598-0.3350.1352-0.4271-0.1969-0.0483-0.27280.6336-0.1255-0.12970.4255-0.04930.07150.3667-0.06120.5081-28.6497-78.640452.4482
372.66030.52350.83952.87380.04964.1544-0.0415-0.3504-0.02860.31070.3153-0.60750.53350.53-0.23660.40890.1001-0.04070.4371-0.15590.60341.0567-23.054486.1985
383.3856-0.81961.97782.67342.13425.36650.14570.3632-0.20.09250.5303-0.97080.07121.2881-0.52430.3718-0.01620.00040.5974-0.2590.76426.496-21.286679.1018
390.8090.21710.91311.2201-0.25221.6727-0.2205-0.24590.129-0.04740.5244-0.5449-0.28820.4648-0.20180.34620.0224-0.03230.5047-0.24910.65691.3255-19.985383.181
408.01993.53863.55937.4041-0.10053.1384-0.868-1.74960.95010.89020.93771.725-1.0189-1.6290.03341.0230.40520.10460.98120.36520.8742-13.5251-11.498121.1033
412.6242-1.22541.15642.5450.77153.2401-0.0347-0.2933-1.18730.25880.6090.05620.85260.0304-0.4370.64750.073-0.23660.4121-0.03241.0448-7.552-15.2898111.3621
425.0031-3.0616-3.68584.79911.23586.4831-0.478-0.3199-2.06030.15960.43520.07911.68230.4320.150.8250.2091-0.25060.6432-0.10541.4063-0.5463-22.4273112.4866
431.34322.503-0.54455.7503-3.5536.2514-0.00330.19670.1088-0.6460.07470.46620.5558-0.2607-0.04170.3622-0.02330.0150.67880.13740.603824.3838-26.396333.0271
445.96082.0228-0.16269.4187-1.55416.05060.0212-0.14370.25270.1147-0.30460.4692-0.4458-0.11490.24040.37710.07390.08070.61170.03590.648924.5082-18.563540.5246
452.2766-1.09480.22573.9553-4.02614.4726-0.04230.14850.42870.22750.04050.3873-0.2712-0.27080.04820.40180.0044-0.00120.56250.05960.772124.3635-21.941937.9984
460.23771.3174-0.66527.9339-3.56011.90320.29710.3610.33980.889-0.3124-0.3636-0.52350.53410.06090.40450.01330.09020.60310.18920.588131.8458-29.007146.922
471.08240.993-0.88421.0242-1.18152.03450.08670.36710.4119-0.2391-0.43930.2414-0.3367-0.01150.41380.57990.1079-0.14590.73550.15330.858723.8061-12.400521.2982
480.5425-0.64771.41242.6898-2.23833.83420.59521.95251.4326-0.9004-0.7273-2.1853-0.08211.68310.22040.7769-0.0950.19891.25060.03781.365943.4913-17.3338-0.5692
494.2908-0.7421-0.8254.1012-0.50612.9701-0.16770.0733-1.2267-0.43670.3731-0.16270.5629-0.1544-0.11840.4782-0.0839-0.07090.72810.06831.097136.6236-18.36969.2177
501.6735-0.2325-1.62333.30760.01952.788-0.25720.277-0.7103-0.28080.5350.84910.828-0.9422-0.26650.6513-0.103-0.07531.10780.15461.224327.1877-21.65228.3602
512.23570.5170.34730.82990.38090.24050.4058-0.1484-0.10881.0497-0.611-0.3094-0.96770.78640.09381.0647-0.4305-0.02480.66050.12020.40899.531741.098873.0561
521.121-1.03960.47091.0771-0.87161.98240.42650.02240.66320.387-0.5318-0.5869-0.53381.36220.3491.4379-0.9514-0.22071.63370.36630.881926.87150.650376.4407
530.9368-2.73422.02328.0735-5.9724.41640.5672-0.357-0.50260.25820.2132-0.10541.3797-0.5393-0.67872.3246-1.1894-0.64223.85330.82372.354546.461955.941392.3887
540.391-0.75290.01181.86560.63051.0318-0.1854-0.5782-0.2950.7578-0.3299-0.36060.81720.66490.6711.6925-0.539-0.0653.16311.20361.707436.700347.453684.8569
551.94151.7089-1.00535.40234.34977.54620.1051-0.6636-0.64050.5594-0.6538-1.25671.53592.24190.53692.1752-1.0275-0.6252.820.92581.45435.011557.549284.2799
569.03283.30156.65329.23554.27135.35830.03611.30290.3501-1.5335-0.1910.1846-1.44740.10330.23942.145-0.223-0.35192.6284-0.1381.77752.747245.246395.6814
574.6436-0.82111.16374.1814-1.69824.08310.54170.21910.2662-0.15830.1552-0.1826-0.1712-0.8293-0.66371.94810.0185-0.13432.53460.6751.325942.64447.223378.6533
588.9458-0.55343.08864.8197-0.35713.51490.1001-0.22570.53030.2142-0.00330.8235-0.0167-0.12530.32570.2970.00360.08740.5013-0.04520.6588-58.3188-64.613865.5663
591.95721.33830.63961.3524-0.21982.2261-0.1576-0.42650.9362-0.01180.01090.8144-0.2417-0.65480.61950.30980.04460.08860.5195-0.10560.9525-69.9175-67.623861.583
606.232-1.3011-2.00877.65630.17852.1470.1684-0.4404-0.5310.35190.0928-0.33020.49940.43330.2060.467-0.0222-0.00880.52530.01140.41-59.5507-78.529164.5621
612.5666-0.0760.65742.6954-0.26695.12280.0318-0.35520.21120.6308-0.03110.41120.1514-0.0135-0.06370.42440.03810.08520.4376-0.10360.5784-59.8678-71.114466.9467
621.67560.3221-0.20591.01980.42310.6591-0.2744-0.24720.42610.00390.17520.26240.0988-0.05390.02330.3445-0.0066-0.04520.4118-0.06710.431-45.0629-68.266760.7145
633.68430.9166-2.2611.7903-1.7524.4261-0.16410.05960.3532-0.08130.17850.0863-0.161-0.02420.10470.33640.0016-0.11480.3459-0.07940.4798-25.52-61.654154.4323
642.55580.2338-2.06922.12120.08813.9851-0.0512-0.23880.13380.09720.2-0.4265-0.03990.21140.08390.3520.0159-0.09180.3937-0.12540.5087-24.8544-62.161558.0107
654.4115-1.8186-1.13314.54772.30336.26530.01260.24290.0042-0.3710.08370.0520.0277-0.2486-0.14190.3345-0.0579-0.02340.26910.0060.38-15.3596-8.401679.297
660.9219-0.24520.04931.57911.04253.93830.0577-0.0471-0.198-0.00620.1214-0.10680.1248-0.1756-0.16240.294-0.01840.00050.2550.04260.5001-13.3675-6.323895.9817
676.79212.05684.70244.28772.72618.1614-0.3275-0.21180.13570.17310.38140.2702-0.26760.3717-0.00020.36970.01960.09150.3126-0.02720.5051-10.29990.735111.5652
684.83930.53712.09592.39870.63415.7697-0.1365-1.41510.00080.50480.0599-0.0793-0.0098-0.02460.07980.56080.0530.02140.7570.030.3906-10.06412.2777123.7366
695.6091.3376-1.61151.6009-0.76632.3674-0.0496-0.26490.19810.3223-0.3884-0.4436-0.2610.94920.32670.4692-0.0512-0.08880.92620.2530.8347.9009-18.538640.4332
701.21980.5099-1.76481.0171-1.20812.8730.0220.0145-0.14010.0059-0.09770.0605-0.26460.08780.00590.3616-0.0948-0.00060.7427-0.00250.75443.6768-12.028716.2208
716.7953-5.11045.41596.8907-3.37386.319-0.1650.23670.1047-0.0081-0.195-0.3609-0.3334-0.09430.33730.3428-0.08940.13930.79320.06960.764646.0696-5.2979.3412
724.5672-1.09081.33663.9314-0.49024.11770.25511.33260.157-0.4666-0.06570.162-0.4795-0.3733-0.16410.5442-0.09090.03021.2940.12170.641346.3684-3.339-2.7411
730.2727-0.0159-0.3230.3389-0.19490.53670.0988-0.61220.09541.0745-0.2384-0.0696-0.89320.5594-0.11292.4914-0.83880.26891.25960.06180.42816.509746.423394.7446
740.1078-0.12660.28240.1564-0.3420.7363-0.3170.62280.47370.031-0.4909-0.543-1.17531.17670.49792.2773-1.113-0.77283.01240.64551.358636.978559.233894.6077
750.9719-0.3164-0.52980.62380.41060.56410.1792-0.64060.32160.28850.3788-0.64730.13070.2631-0.29442.5656-1.2138-0.96032.3970.26832.062938.213471.378592.597
760.4519-0.35030.67290.3954-0.42892.739-0.19720.30610.33340.2071-0.147-0.3358-0.31510.43080.2642.7421-1.3744-1.03612.4690.84131.711733.73857.763993.4915
772.7661-0.9966-1.3980.37990.49890.72690.23110.3121-0.5514-0.57310.02440.48430.7261-1.0668-0.20372.1529-0.3554-0.39312.20880.69772.781550.337873.461486.7953
788.70030.9402-7.86140.1034-0.85487.1060.05120.30170.20370.2206-0.39980.0797-0.0139-0.08820.27922.5022-1.127-0.69463.41490.47891.817842.773467.0562101.0272
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and ( resseq 43:57 )A43 - 57
2X-RAY DIFFRACTION2chain A and ( resseq 58:79 )A58 - 79
3X-RAY DIFFRACTION3chain A and ( resseq 80:104 )A80 - 104
4X-RAY DIFFRACTION4chain A and ( resseq 105:136 )A105 - 136
5X-RAY DIFFRACTION5chain A and ( resseq 137:163 )A137 - 163
6X-RAY DIFFRACTION6chain A and ( resseq 164:184 )A164 - 184
7X-RAY DIFFRACTION7chain A and ( resseq 185:201 )A185 - 201
8X-RAY DIFFRACTION8chain A and ( resseq 202:228 )A202 - 228
9X-RAY DIFFRACTION9chain A and ( resseq 229:247 )A229 - 247
10X-RAY DIFFRACTION10chain A and ( resseq 248:274 )A248 - 274
11X-RAY DIFFRACTION11chain A and ( resseq 275:294 )A275 - 294
12X-RAY DIFFRACTION12chain A and ( resseq 295:309 )A295 - 309
13X-RAY DIFFRACTION13chain B and ( resseq 43:57 )B43 - 57
14X-RAY DIFFRACTION14chain B and ( resseq 58:79 )B58 - 79
15X-RAY DIFFRACTION15chain B and ( resseq 80:104 )B80 - 104
16X-RAY DIFFRACTION16chain B and ( resseq 105:122 )B105 - 122
17X-RAY DIFFRACTION17chain B and ( resseq 123:163 )B123 - 163
18X-RAY DIFFRACTION18chain B and ( resseq 164:201 )B164 - 201
19X-RAY DIFFRACTION19chain B and ( resseq 202:228 )B202 - 228
20X-RAY DIFFRACTION20chain B and ( resseq 229:274 )B229 - 274
21X-RAY DIFFRACTION21chain B and ( resseq 275:294 )B275 - 294
22X-RAY DIFFRACTION22chain B and ( resseq 295:309 )B295 - 309
23X-RAY DIFFRACTION23chain C and ( resseq 44:57 )C44 - 57
24X-RAY DIFFRACTION24chain C and ( resseq 58:228 )C58 - 228
25X-RAY DIFFRACTION25chain C and ( resseq 229:274 )C229 - 274
26X-RAY DIFFRACTION26chain C and ( resseq 275:294 )C275 - 294
27X-RAY DIFFRACTION27chain C and ( resseq 295:308 )C295 - 308
28X-RAY DIFFRACTION28chain D and ( resseq 44:57 )D44 - 57
29X-RAY DIFFRACTION29chain D and ( resseq 58:228 )D58 - 228
30X-RAY DIFFRACTION30chain D and ( resseq 229:274 )D229 - 274
31X-RAY DIFFRACTION31chain D and ( resseq 275:294 )D275 - 294
32X-RAY DIFFRACTION32chain D and ( resseq 295:309 )D295 - 309
33X-RAY DIFFRACTION33chain H and ( resseq 2:35C )H2 - 35
34X-RAY DIFFRACTION34chain H and ( resseq 35D:119 )H35 - 119
35X-RAY DIFFRACTION35chain H and ( resseq 120:139 )H120 - 139
36X-RAY DIFFRACTION36chain H and ( resseq 140:213 )H140 - 213
37X-RAY DIFFRACTION37chain I and ( resseq 2:44 )I2 - 44
38X-RAY DIFFRACTION38chain I and ( resseq 45:82 )I45 - 82
39X-RAY DIFFRACTION39chain I and ( resseq 83:119 )I83 - 119
40X-RAY DIFFRACTION40chain I and ( resseq 120:139 )I120 - 139
41X-RAY DIFFRACTION41chain I and ( resseq 140:198 )I140 - 198
42X-RAY DIFFRACTION42chain I and ( resseq 199:212 )I199 - 212
43X-RAY DIFFRACTION43chain J and ( resseq 2:35C )J2 - 35
44X-RAY DIFFRACTION44chain J and ( resseq 35D:75 )J35 - 75
45X-RAY DIFFRACTION45chain J and ( resseq 76:100E )J76 - 100
46X-RAY DIFFRACTION46chain J and ( resseq 100F:103 )J100 - 103
47X-RAY DIFFRACTION47chain J and ( resseq 104:119 )J104 - 119
48X-RAY DIFFRACTION48chain J and ( resseq 120:139 )J120 - 139
49X-RAY DIFFRACTION49chain J and ( resseq 140:198 )J140 - 198
50X-RAY DIFFRACTION50chain J and ( resseq 199:212 )J199 - 212
51X-RAY DIFFRACTION51chain K and ( resseq 2:100O )K2 - 100
52X-RAY DIFFRACTION52chain K and ( resseq 100P:124 )K100 - 124
53X-RAY DIFFRACTION53chain K and ( resseq 125:144 )K125 - 144
54X-RAY DIFFRACTION54chain K and ( resseq 145:164 )K145 - 164
55X-RAY DIFFRACTION55chain K and ( resseq 165:184 )K165 - 184
56X-RAY DIFFRACTION56chain K and ( resseq 185:193 )K185 - 193
57X-RAY DIFFRACTION57chain K and ( resseq 194:212 )K194 - 212
58X-RAY DIFFRACTION58chain L and ( resseq 1:18 )L1 - 18
59X-RAY DIFFRACTION59chain L and ( resseq 19:32 )L19 - 32
60X-RAY DIFFRACTION60chain L and ( resseq 33:61 )L33 - 61
61X-RAY DIFFRACTION61chain L and ( resseq 62:90 )L62 - 90
62X-RAY DIFFRACTION62chain L and ( resseq 91:121 )L91 - 121
63X-RAY DIFFRACTION63chain L and ( resseq 122:161 )L122 - 161
64X-RAY DIFFRACTION64chain L and ( resseq 162:212 )L162 - 212
65X-RAY DIFFRACTION65chain M and ( resseq 1:61 )M1 - 61
66X-RAY DIFFRACTION66chain M and ( resseq 62:141 )M62 - 141
67X-RAY DIFFRACTION67chain M and ( resseq 142:181 )M142 - 181
68X-RAY DIFFRACTION68chain M and ( resseq 182:212 )M182 - 212
69X-RAY DIFFRACTION69chain N and ( resseq 1:90 )N1 - 90
70X-RAY DIFFRACTION70chain N and ( resseq 91:141 )N91 - 141
71X-RAY DIFFRACTION71chain N and ( resseq 142:181 )N142 - 181
72X-RAY DIFFRACTION72chain N and ( resseq 182:212 )N182 - 212
73X-RAY DIFFRACTION73chain O and ( resseq 1:101 )O1 - 101
74X-RAY DIFFRACTION74chain O and ( resseq 102:143 )O102 - 143
75X-RAY DIFFRACTION75chain O and ( resseq 144:163 )O144 - 163
76X-RAY DIFFRACTION76chain O and ( resseq 164:183 )O164 - 183
77X-RAY DIFFRACTION77chain O and ( resseq 184:193 )O184 - 193
78X-RAY DIFFRACTION78chain O and ( resseq 194:212 )O194 - 212

+
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