[English] 日本語
Yorodumi
- PDB-5uqy: Crystal structure of Marburg virus GP in complex with the human s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uqy
TitleCrystal structure of Marburg virus GP in complex with the human survivor antibody MR78
Components
  • (ENVELOPE GLYCOPROTEIN ...) x 2
  • MR78 Fab heavy chain
  • MR78 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / glycoprotein / viral protein / antibody / Fab / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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
Similarity search - Function
TLV/ENV coat polyprotein / : / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Envelope glycoprotein
Similarity search - Component
Biological speciesLake Victoria marburgvirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsHashiguchi, T. / Fusco, M.L. / Hastie, K.M. / Bomholdt, Z.A. / Lee, J.E. / Flyak, A.I. / Matsuoka, R. / Kohda, D. / Yanagi, Y. / Hammel, M. ...Hashiguchi, T. / Fusco, M.L. / Hastie, K.M. / Bomholdt, Z.A. / Lee, J.E. / Flyak, A.I. / Matsuoka, R. / Kohda, D. / Yanagi, Y. / Hammel, M. / Crowe, J.E. / Saphire, E.O.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI109762 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI089498 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI069347 United States
CitationJournal: Cell / Year: 2015
Title: Structural basis for Marburg virus neutralization by a cross-reactive human antibody.
Authors: Hashiguchi, T. / Fusco, M.L. / Bornholdt, Z.A. / Lee, J.E. / Flyak, A.I. / Matsuoka, R. / Kohda, D. / Yanagi, Y. / Hammel, M. / Crowe, J.E. / Saphire, E.O.
History
DepositionFeb 8, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMar 1, 2017ID: 3X2D
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 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 / 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.label_asym_id / _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 2.1Oct 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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENVELOPE GLYCOPROTEIN GP1
B: ENVELOPE GLYCOPROTEIN GP2
C: MR78 Fab light chain
D: MR78 Fab heavy chain
E: ENVELOPE GLYCOPROTEIN GP1
F: ENVELOPE GLYCOPROTEIN GP2
G: MR78 Fab light chain
H: MR78 Fab heavy chain
I: ENVELOPE GLYCOPROTEIN GP1
J: ENVELOPE GLYCOPROTEIN GP2
K: MR78 Fab light chain
L: MR78 Fab heavy chain
M: ENVELOPE GLYCOPROTEIN GP1
N: ENVELOPE GLYCOPROTEIN GP2
O: MR78 Fab light chain
P: MR78 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)412,48430
Polymers404,80216
Non-polymers7,68214
Water00
1
A: ENVELOPE GLYCOPROTEIN GP1
B: ENVELOPE GLYCOPROTEIN GP2
C: MR78 Fab light chain
D: MR78 Fab heavy chain
hetero molecules

A: ENVELOPE GLYCOPROTEIN GP1
B: ENVELOPE GLYCOPROTEIN GP2
C: MR78 Fab light chain
D: MR78 Fab heavy chain
hetero molecules

A: ENVELOPE GLYCOPROTEIN GP1
B: ENVELOPE GLYCOPROTEIN GP2
C: MR78 Fab light chain
D: MR78 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,36721
Polymers303,60212
Non-polymers5,7659
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area42380 Å2
ΔGint-279 kcal/mol
Surface area88850 Å2
MethodPISA
2
E: ENVELOPE GLYCOPROTEIN GP1
F: ENVELOPE GLYCOPROTEIN GP2
G: MR78 Fab light chain
H: MR78 Fab heavy chain
I: ENVELOPE GLYCOPROTEIN GP1
J: ENVELOPE GLYCOPROTEIN GP2
K: MR78 Fab light chain
L: MR78 Fab heavy chain
M: ENVELOPE GLYCOPROTEIN GP1
N: ENVELOPE GLYCOPROTEIN GP2
O: MR78 Fab light chain
P: MR78 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,36223
Polymers303,60212
Non-polymers5,76011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39180 Å2
ΔGint-244 kcal/mol
Surface area83470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.653, 204.653, 192.963
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

-
ENVELOPE GLYCOPROTEIN ... , 2 types, 8 molecules AEIMBFJN

#1: Protein
ENVELOPE GLYCOPROTEIN GP1 / GP1 / 2 / GP / Virion spike glycoprotein


Mass: 27885.434 Da / Num. of mol.: 4 / Fragment: UNP residues 17-256, 426-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus (strain Ravn-87)
Strain: Ravn-87 / Gene: GP / Plasmid: pMT / Cell line (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: Q1PDC7
#2: Protein
ENVELOPE GLYCOPROTEIN GP2 / GP1 / 2 / GP / Virion spike glycoprotein


Mass: 26137.631 Da / Num. of mol.: 4 / Fragment: UNP residues 436-637
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus (strain Ravn-87)
Strain: Ravn-87 / Gene: GP / Plasmid: pMT / Cell line (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: Q1PDC7

-
Antibody , 2 types, 8 molecules CGKODHLP

#3: Antibody
MR78 Fab light chain


Mass: 23307.877 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: Hybridoma / Plasmid details: B cell hybrdoma
#4: Antibody
MR78 Fab heavy chain


Mass: 23869.578 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: Hybridoma / Plasmid details: B cell hybrdoma

-
Sugars , 6 types, 14 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.: 6
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: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]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-f1_d2-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE
#9: 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.: 1
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
#10: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M NaCl, 0.05 M MES pH6.5, 13 % PEG4000, 0.5 % ethyl acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.6→130.53 Å / Num. obs: 52806 / % possible obs: 99.4 % / Redundancy: 5.1 % / CC1/2: 0.994 / Rsym value: 0.144 / Net I/σ(I): 12.9
Reflection shellResolution: 3.6→3.612 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 534 / Rsym value: 0.94 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CSY

3csy


Resolution: 3.6→84.739 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.52
RfactorNum. reflection% reflection
Rfree0.262 2674 5.07 %
Rwork0.2212 --
obs0.2233 52782 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.6→84.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20699 0 509 0 21208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221750
X-RAY DIFFRACTIONf_angle_d0.53229644
X-RAY DIFFRACTIONf_dihedral_angle_d12.03112976
X-RAY DIFFRACTIONf_chiral_restr0.0393453
X-RAY DIFFRACTIONf_plane_restr0.0043690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6004-3.66580.33771370.31142635X-RAY DIFFRACTION100
3.6658-3.73640.33671470.30182650X-RAY DIFFRACTION100
3.7364-3.81260.36661540.27522617X-RAY DIFFRACTION100
3.8126-3.89550.28341380.26512613X-RAY DIFFRACTION100
3.8955-3.98610.29341510.25222621X-RAY DIFFRACTION100
3.9861-4.08580.29141290.24882656X-RAY DIFFRACTION100
4.0858-4.19630.29411360.23382644X-RAY DIFFRACTION99
4.1963-4.31980.32231460.23612619X-RAY DIFFRACTION100
4.3198-4.45920.23961360.21632643X-RAY DIFFRACTION100
4.4592-4.61860.26371340.21782641X-RAY DIFFRACTION100
4.6186-4.80350.22981290.20452667X-RAY DIFFRACTION100
4.8035-5.0220.26051430.2132621X-RAY DIFFRACTION99
5.022-5.28680.25761390.21412622X-RAY DIFFRACTION100
5.2868-5.6180.26741550.20182647X-RAY DIFFRACTION100
5.618-6.05160.2581460.2042636X-RAY DIFFRACTION99
6.0516-6.66040.21821480.20162629X-RAY DIFFRACTION99
6.6604-7.62360.25831410.20472652X-RAY DIFFRACTION99
7.6236-9.60280.18031260.18942640X-RAY DIFFRACTION99
9.6028-84.76270.25471390.21372655X-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://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