[English] 日本語
Yorodumi
- PDB-6eay: Structural Basis for Broad Neutralization of Ebolaviruses by an A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6eay
TitleStructural Basis for Broad Neutralization of Ebolaviruses by an Antibody Targeting the Glycoprotein Fusion Loop
Components
  • (Envelope glycoprotein) x 2
  • CA45 heavy chain
  • CA45 light chain
KeywordsVIRAL PROTEIN / ebolavirus / glycoprotein / cross-protective antibody / broadly neutralizing antibody / CA45 / fusion loop / cross-reactive / filovirus
Function / homology
Function and homology information


host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / membrane raft / symbiont entry into host cell / fusion of virus membrane with host endosome membrane ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / membrane raft / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesMacaca fascicularis (crab-eating macaque)
Zaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.72 Å
AuthorsJanus, B.M. / Ofek, G.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for broad neutralization of ebolaviruses by an antibody targeting the glycoprotein fusion loop.
Authors: Janus, B.M. / van Dyk, N. / Zhao, X. / A Howell, K. / Soto, C. / Aman, M.J. / Li, Y. / Fuerst, T.R. / Ofek, G.
History
DepositionAug 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 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 / 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_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: CA45 light chain
H: CA45 heavy chain
A: Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2577
Polymers102,4174
Non-polymers1,8403
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11850 Å2
ΔGint-31 kcal/mol
Surface area37000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.429, 153.429, 335.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

-
Protein , 2 types, 2 molecules AB

#3: Protein Envelope glycoprotein / GP1 / 2 / GP


Mass: 18636.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: GP / Cell line (production host): HEK293S GNTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q05320
#4: Protein Envelope glycoprotein / GP1 / 2 / GP


Mass: 35319.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: GP / Cell line (production host): HEK293S GNTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q05320

-
Antibody , 2 types, 2 molecules LH

#1: Antibody CA45 light chain


Mass: 23291.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell: B cell / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#2: Antibody CA45 heavy chain


Mass: 25169.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell: B cell / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)

-
Sugars , 2 types, 3 molecules

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


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}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.: 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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 73.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1M Potassium Sodium Tartrate, 0.1M MES pH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.72→76.71 Å / Num. obs: 14037 / % possible obs: 87.2 % / Redundancy: 9.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.054 / Net I/σ(I): 9.9
Reflection shellResolution: 3.72→4.07 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1402 / CC1/2: 0.859 / Rpim(I) all: 0.176 / % possible all: 88.5

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3228: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JQ3, 3Q6G

5jq3

3q6g


Resolution: 3.72→45.128 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2966 695 4.96 %Random
Rwork0.2586 ---
obs0.2604 14025 85.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.72→45.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5254 0 122 0 5376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025518
X-RAY DIFFRACTIONf_angle_d0.577583
X-RAY DIFFRACTIONf_dihedral_angle_d17.9011858
X-RAY DIFFRACTIONf_chiral_restr0.046899
X-RAY DIFFRACTIONf_plane_restr0.004966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7201-4.00720.34671380.33012656X-RAY DIFFRACTION87
4.0072-4.41020.23741470.26392690X-RAY DIFFRACTION88
4.4102-5.04760.26571480.24222645X-RAY DIFFRACTION86
5.0476-6.35660.37691100.27472687X-RAY DIFFRACTION85
6.3566-45.13150.29221520.23022652X-RAY DIFFRACTION83
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)
17.8275.87463.48065.84870.07658.0013-1.37551.6747-0.0065-1.57740.85991.7875-0.97580.95820.32961.4445-0.2878-0.05950.84690.00131.799729.6068-62.7008-54.9724
27.85615.13014.607610.19973.24636.1205-0.14030.3948-0.2381-0.41690.305-0.7246-0.13970.8638-0.20950.626-0.0228-0.10140.6334-0.07791.386533.9795-63.9597-46.0674
36.86694.9577-3.65936.2865-4.99518.822-0.76450.33550.9203-2.0510.16030.42160.92781.13170.52881.0673-0.2289-0.29380.86470.16961.747429.0615-60.6322-47.4949
45.97672.0104-0.06163.24591.35294.42560.7647-1.06480.77950.267-0.6231.0584-0.4316-0.052-0.16291.0407-0.21480.20190.8946-0.20982.56662.4508-70.2363-35.7268
57.3294-2.9152-0.72642.3527-1.22142.47680.8685-0.50870.338-0.7249-0.97644.30831.0717-1.45130.50150.4091-0.31710.84591.1735-0.65583.064-6.904-70.2824-32.7785
67.6656-6.5682-0.77045.91771.20885.2582-1.1829-0.66911.80490.82380.5361.403-0.5455-0.2850.5790.626-0.0296-0.26670.66370.00341.460630.6248-45.4169-30.6914
74.84444.2744-0.3783.7183-0.79992.8385-1.05240.0294-1.1286-0.15250.80580.6973-0.1375-0.08590.38290.7961-0.1778-0.34980.75490.27142.152529.2086-46.7591-41.8874
82.10561.3668-0.10481.694-0.73422.4863-0.41180.32680.5755-0.2562-0.34311.3382-0.67950.59680.47970.7533-0.301-0.33280.5087-0.05613.032532.1449-47.1664-38.2661
95.8554-4.03061.09122.6144-0.83581.81540.4907-0.73581.03541.6045-0.85750.10330.13250.00010.39321.2045-0.35950.07121.22-0.26932.09369.5037-59.3324-25.8737
108.0842-4.5945-1.10163.8733-2.89568.56310.9424-0.7239-0.2682-0.4869-0.9480.8308-0.00230.524-0.04151.094-0.2080.05071.08-0.10081.75287.9309-61.6136-22.6324
119.6810.15620.45995.76113.63579.0449-0.58950.6658-0.1243-1.4372-0.4246-0.246-0.5809-0.19590.86680.4204-0.1385-0.01710.7885-0.16011.523354.1872-58.5193-35.8214
125.9001-5.8998-0.86541.999-2.09031.82783.48332.0173-3.1659-2.0448-0.1825.18743.49441.8001-3.11111.20080.4166-0.19951.07730.15111.607951.7226-28.39-32.1063
132.845-0.3981-1.28343.99272.20254.07630.10290.0962-0.32070.5431-0.25960.33950.5252-0.39590.2110.4685-0.06890.01910.41920.12241.131959.1797-53.2033-32.4941
145.21931.5676-4.63485.0359-5.24377.8540.2507-0.81590.2287-0.65971.33121.13681.5052-0.1729-1.03980.4326-0.1869-0.03530.63230.23740.960175.1582-50.9146-38.4799
158.2198-2.0556-4.93035.3725.71867.15040.11822.2006-2.22331.5964-0.48081.79071.911-2.68840.6421.6742-0.13710.16371.6206-0.51952.235576.0115-50.3201-63.1621
161.9814-4.53567.9618.25860.11736.67371.06627.4046-0.4221-2.98760.02640.43980.63490.9358-0.56841.1513-0.0015-0.35891.5021-0.09640.959165.2416-60.0269-46.7422
172.05432.1347-2.22933.5432-2.47056.4425-0.20270.11440.14920.29480.57310.4397-0.0198-1.1143-0.29540.4864-0.0818-0.00030.51480.05491.351161.6212-60.3306-30.906
183.8568-1.44082.9673.1645-1.71027.973-0.3874-0.41960.12240.2770.1799-0.0781-0.8842-0.29020.19640.5062-0.017-0.06680.5241-0.08821.252164.7909-57.43-16.2361
193.99041.2803-5.64942.6422-0.25988.3391-0.3908-0.3791-0.46110.234-0.03430.21940.44080.12830.37040.3640.00080.04180.35240.0530.900963.2355-58.0129-19.7391
204.3869-3.26853.60592.2881-2.45833.2111-1.0381-2.72460.07381.43691.46110.4697-1.9519-0.6982-0.98290.6073-0.24610.29590.68850.09341.49250.6052-55.6845-16.2867
215.4405-0.18182.25049.9162-0.66271.6951-0.35590.7466-0.1931.3603-1.0526-2.45581.30060.32280.97460.6329-0.22690.23350.89970.17461.058752.9586-68.7567-5.5561
225.93165.31615.29799.99677.54716.25340.84581.9119-0.236-2.13411.42730.1557-1.67640.3111-1.34571.0553-0.2166-0.1162-0.01550.62232.068840.8507-64.1281-9.8468
235.7077-5.46220.05367.8441-4.7498.96540.4269-0.45240.9777-0.83260.43412.1080.747-0.8897-0.93560.68750.03280.29270.79540.40922.051841.8123-68.84660.9783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 2 through 33 )
2X-RAY DIFFRACTION2chain 'L' and (resid 34 through 75 )
3X-RAY DIFFRACTION3chain 'L' and (resid 76 through 102 )
4X-RAY DIFFRACTION4chain 'L' and (resid 103 through 172 )
5X-RAY DIFFRACTION5chain 'L' and (resid 173 through 212 )
6X-RAY DIFFRACTION6chain 'H' and (resid 2 through 33 )
7X-RAY DIFFRACTION7chain 'H' and (resid 34 through 52 )
8X-RAY DIFFRACTION8chain 'H' and (resid 73 through 113 )
9X-RAY DIFFRACTION9chain 'H' and (resid 114 through 169 )
10X-RAY DIFFRACTION10chain 'H' and (resid 170 through 208 )
11X-RAY DIFFRACTION11chain 'A' and (resid 502 through 524 )
12X-RAY DIFFRACTION12chain 'A' and (resid 525 through 529 )
13X-RAY DIFFRACTION13chain 'A' and (resid 530 through 575 )
14X-RAY DIFFRACTION14chain 'A' and (resid 576 through 596 )
15X-RAY DIFFRACTION15chain 'A' and (resid 597 through 614 )
16X-RAY DIFFRACTION16chain 'B' and (resid 32 through 50 )
17X-RAY DIFFRACTION17chain 'B' and (resid 51 through 89 )
18X-RAY DIFFRACTION18chain 'B' and (resid 90 through 126 )
19X-RAY DIFFRACTION19chain 'B' and (resid 127 through 185 )
20X-RAY DIFFRACTION20chain 'B' and (resid 186 through 223 )
21X-RAY DIFFRACTION21chain 'B' and (resid 224 through 249 )
22X-RAY DIFFRACTION22chain 'B' and (resid 250 through 260 )
23X-RAY DIFFRACTION23chain 'B' and (resid 261 through 280 )

+
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