[English] 日本語
Yorodumi
- PDB-6bp2: Therapeutic human monoclonal antibody MR191 bound to a marburgvir... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bp2
TitleTherapeutic human monoclonal antibody MR191 bound to a marburgvirus glycoprotein
Components
  • Envelope glycoprotein
  • Envelope glycoprotein GP2
  • MR191 Fab Heavy Chain
  • MR191 Fab Light Chain
KeywordsVIRAL PROTEIN/immune system / Marburg / Ravn / Glycoprotein / Complex / VIRAL PROTEIN / VIRAL PROTEIN-immune system complex
Function / homology
Function and homology information


membrane => GO:0016020 / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / plasma membrane
Similarity search - Function
TLV/ENV coat polyprotein / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein / Envelope glycoprotein
Similarity search - Component
Biological speciesMarburg marburgvirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.172 Å
AuthorsKing, L.B. / Fusco, M.L. / Flyak, A.I. / Ilinykh, P.A. / Huang, K. / Gunn, B. / Kirchdoerfer, R.N. / Hastie, K.M. / Sangha, A.K. / Meiler, J. ...King, L.B. / Fusco, M.L. / Flyak, A.I. / Ilinykh, P.A. / Huang, K. / Gunn, B. / Kirchdoerfer, R.N. / Hastie, K.M. / Sangha, A.K. / Meiler, J. / Alter, G. / Bukreyev, A. / Crowe, J.E.J. / Saphire, E.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI089498 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI109762 United States
CitationJournal: Cell Host Microbe / Year: 2018
Title: The Marburgvirus-Neutralizing Human Monoclonal Antibody MR191 Targets a Conserved Site to Block Virus Receptor Binding.
Authors: King, L.B. / Fusco, M.L. / Flyak, A.I. / Ilinykh, P.A. / Huang, K. / Gunn, B. / Kirchdoerfer, R.N. / Hastie, K.M. / Sangha, A.K. / Meiler, J. / Alter, G. / Bukreyev, A. / Crowe, J.E. / Saphire, E.O.
History
DepositionNov 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 2.0Mar 7, 2018Group: Advisory / Atomic model / Derived calculations
Category: atom_site / pdbx_unobs_or_zero_occ_atoms ...atom_site / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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.auth_asym_id / _atom_site.auth_seq_id ..._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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 3.1Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope glycoprotein
B: Envelope glycoprotein GP2
H: MR191 Fab Heavy Chain
L: MR191 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6138
Polymers97,6734
Non-polymers1,9404
Water00
1
A: Envelope glycoprotein
B: Envelope glycoprotein GP2
H: MR191 Fab Heavy Chain
L: MR191 Fab Light Chain
hetero molecules

A: Envelope glycoprotein
B: Envelope glycoprotein GP2
H: MR191 Fab Heavy Chain
L: MR191 Fab Light Chain
hetero molecules

A: Envelope glycoprotein
B: Envelope glycoprotein GP2
H: MR191 Fab Heavy Chain
L: MR191 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,83824
Polymers293,01912
Non-polymers5,81912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_745-y+2,x-y-1,z1
crystal symmetry operation3_875-x+y+3,-x+2,z1
Buried area51380 Å2
ΔGint-172 kcal/mol
Surface area93880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.796, 133.796, 151.003
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Envelope glycoprotein


Mass: 27885.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marburg marburgvirus / Gene: GP, DF49_53427gpGP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A0U2XLP5, UniProt: Q1PDC7*PLUS
#2: Protein Envelope glycoprotein GP2


Mass: 22560.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marburg marburgvirus / Gene: GP, DF49_53427gpGP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A0U2XLP5, UniProt: Q1PDC7*PLUS

-
Antibody , 2 types, 2 molecules HL

#3: Antibody MR191 Fab Heavy Chain


Mass: 24375.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Nicotiana benthamiana (plant)
#4: Antibody MR191 Fab Light Chain


Mass: 22851.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Nicotiana benthamiana (plant)

-
Sugars , 3 types, 4 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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.: 2
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)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 5% PEG 3000, 26% PEG 400, 6% Glycerol
Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.17→46.17 Å / Num. obs: 26795 / % possible obs: 99.28 % / Redundancy: 11 % / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Rrim(I) all: 0.17 / Net I/σ(I): 12.4
Reflection shellResolution: 3.17→3.29 Å / Redundancy: 11.5 % / Rmerge(I) obs: 2.02 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2652 / % possible all: 98.38

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X2D

3x2d
PDB Unreleased entry


Resolution: 3.172→46.167 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2837 1361 5.09 %
Rwork0.252 --
obs0.2536 26728 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.172→46.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 128 0 5684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135830
X-RAY DIFFRACTIONf_angle_d1.6517938
X-RAY DIFFRACTIONf_dihedral_angle_d10.5172112
X-RAY DIFFRACTIONf_chiral_restr0.082929
X-RAY DIFFRACTIONf_plane_restr0.013997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1718-3.28520.41281350.39162464X-RAY DIFFRACTION98
3.2852-3.41670.41081170.37342540X-RAY DIFFRACTION99
3.4167-3.57210.32891510.34252481X-RAY DIFFRACTION100
3.5721-3.76040.3631040.30912539X-RAY DIFFRACTION100
3.7604-3.99580.33731210.28072537X-RAY DIFFRACTION99
3.9958-4.30410.26981730.24632499X-RAY DIFFRACTION100
4.3041-4.73690.28541390.20922539X-RAY DIFFRACTION100
4.7369-5.42140.26611450.22732566X-RAY DIFFRACTION100
5.4214-6.82690.26911240.24042579X-RAY DIFFRACTION99
6.8269-46.17140.23371520.21352623X-RAY DIFFRACTION97

+
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