[English] 日本語
Yorodumi
- PDB-4mmu: Crystal Structure of Prefusion-stabilized RSV F Variant DS-Cav1 a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mmu
TitleCrystal Structure of Prefusion-stabilized RSV F Variant DS-Cav1 at pH 5.5
Components(Fusion glycoprotein ...) x 2
KeywordsVIRAL PROTEIN / fusion / membrane / structure-based vaccine design
Function / homology
Function and homology information


Translation of respiratory syncytial virus mRNAs / symbiont-mediated induction of syncytium formation / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / virion component / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell ...Translation of respiratory syncytial virus mRNAs / symbiont-mediated induction of syncytium formation / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / virion component / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
PHOSPHATE ION / Fusion glycoprotein F0 / Fibritin
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A2
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJoyce, M.G. / Mclellan, J.S. / Stewart-Jones, G.B.E. / Sastry, M. / Yang, Y. / Graham, B.S. / Kwong, P.D.
CitationJournal: Science / Year: 2013
Title: Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus.
Authors: McLellan, J.S. / Chen, M. / Joyce, M.G. / Sastry, M. / Stewart-Jones, G.B. / Yang, Y. / Zhang, B. / Chen, L. / Srivatsan, S. / Zheng, A. / Zhou, T. / Graepel, K.W. / Kumar, A. / Moin, S. / ...Authors: McLellan, J.S. / Chen, M. / Joyce, M.G. / Sastry, M. / Stewart-Jones, G.B. / Yang, Y. / Zhang, B. / Chen, L. / Srivatsan, S. / Zheng, A. / Zhou, T. / Graepel, K.W. / Kumar, A. / Moin, S. / Boyington, J.C. / Chuang, G.Y. / Soto, C. / Baxa, U. / Bakker, A.Q. / Spits, H. / Beaumont, T. / Zheng, Z. / Xia, N. / Ko, S.Y. / Todd, J.P. / Rao, S. / Graham, B.S. / Kwong, P.D.
History
DepositionSep 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.2Sep 20, 2017Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jun 2, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Sep 20, 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
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5258
Polymers54,8252
Non-polymers7006
Water1,45981
1
A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain
hetero molecules

A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain
hetero molecules

A: Fusion glycoprotein F2
B: Fusion glycoprotein F1 fused with Fibritin trimerization domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,57524
Polymers164,4746
Non-polymers2,10118
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area44620 Å2
ΔGint-457 kcal/mol
Surface area52170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.588, 168.588, 168.588
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

-
Components

-
Fusion glycoprotein ... , 2 types, 2 molecules AB

#1: Protein Fusion glycoprotein F2


Mass: 9215.410 Da / Num. of mol.: 1 / Mutation: P102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2 / Gene: F / Plasmid: p(alpha)H / Cell line (production host): FreeStyle(tm) 293-F / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Protein Fusion glycoprotein F1 fused with Fibritin trimerization domain


Mass: 45609.148 Da / Num. of mol.: 1 / Mutation: S155C, S190F, V207L, S290C, I379V, M447V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human respiratory syncytial virus A2, (gene. exp.) Enterobacteria phage T4 (virus)
Gene: F / Plasmid: p(alpha)H / Cell line (production host): FreeStyle(tm) 293-F / Production host: Homo sapiens (human) / References: UniProt: P03420, UniProt: P10104

-
Sugars , 1 types, 1 molecules

#4: 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

-
Non-polymers , 3 types, 86 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growpH: 5.5
Details: 1.8 M Ammonium sulphate 0.1 M citrate pH5.5, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 2, 2013 / Details: SI 111
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 16922 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 16.3 % / Biso Wilson estimate: 74.39 Å2 / Rmerge(I) obs: 0.22 / Rsym value: 0.22 / Net I/σ(I): 22.4

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JHW

4jhw


Resolution: 3→28.5 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.737 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 859 5.08 %RANDOM
Rwork0.178 ---
obs0.181 16922 99.8 %-
all-16956 --
Displacement parametersBiso mean: 78.06 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 3→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 39 81 3642
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013607HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.434890HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1275SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes97HARMONIC2
X-RAY DIFFRACTIONt_gen_planes501HARMONIC5
X-RAY DIFFRACTIONt_it3607HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion24.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion499SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4268SEMIHARMONIC4
LS refinement shellResolution: 3→3.18 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3027 131 4.94 %
Rwork0.2329 2519 -
all0.2364 2650 -
obs--99.81 %
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)
16.3247-1.9265-1.244904.37642.5659-0.2137-0.9749-0.45790.80380.24310.18010.24020.2716-0.0294-0.13270.07520.024-0.03050.1357-0.1468168.423180.516205.324
21.7017-0.1939-0.73032.55884.0548.42350.23160.4289-0.39260.16610.2842-0.07370.97420.1323-0.51580.11380.0214-0.1541-0.0769-0.0466-0.0347172.573151.832168.77
30-2.5762-2.550202.08485.17720.00440.6884-0.3213-0.2501-0.2434-0.19380.7267-0.04610.239-0.1458-0.1935-0.2155-0.1939-0.2561-0.2592172.03152.954152.737
40.16614.31877.802405.94640-0.00740.9145-0.1187-0.36910.15350.36890.205-0.3768-0.14610.7150.1021-0.08380.0211-0.15550.09188.279163.838171.934
50.15311.7852.18340-0.87682.42160.22560.4232-0.4578-0.85990.07710.17010.44990.8178-0.3027-0.03950.1923-0.1636-0.119-0.1114-0.2117187.352160.199179.797
66.93613.94823.72696.7731-1.4955.6002-0.1935-0.2732-1.1824-0.29070.29810.13951.20420.6824-0.10460.72290.1522-0.1801-0.3851-0.0036-0.0235178.878140.192175.063
71.9068-0.6779-0.15664.21565.21680-0.00060.2834-0.58340.09390.15970.1590.55220.1037-0.15910.3253-0.3301-0.154-0.3252-0.2824-0.116167.441140.976158.727
83.4223.9562.07651.66630.9374.86840.03940.30740.0836-0.3199-0.0011-0.03940.49530.109-0.03830.3724-0.255-0.32160.2018-0.44920.0692161.451141.137144.913
92.2725-2.5931.95110.00331.12550-0.17520.1969-0.09480.28340.22160.5360.5413-0.3465-0.0464-0.1109-0.2207-0.2022-0.2276-0.2529-0.1478165.255153.149160.075
103.9629-2.0658-2.67482.92281.94995.9833-0.3041-0.5081-0.74470.57290.0270.21330.8588-0.14240.27710.1902-0.153-0.2158-0.1792-0.07740.0764170.721154.278178.652
110.55821.20230.75940-0.55763.1089-0.010.1674-0.4127-0.02350.21760.34370.932-0.1708-0.20750.26020.0038-0.1423-0.0075-0.03290.1936174.025156.093182.203
1212.29084.0412-0.08861.40233.40877.1812-0.1329-0.31861.0274-0.44420.13150.6057-0.82050.04960.0015-0.17050.0592-0.0097-0.2018-0.0625-0.2497177.026194.042199.428
134.6389-0.08860.45454.8132-0.27062.308-0.1814-0.09890.22190.17680.02530.21530.2119-0.25390.156-0.14780.03310.0006-0.08740.1276-0.1153178.692172.546199.324
145.3248-1.05512.8165.49966.18280.0434-0.10480.0664-0.0891-0.2505-0.00770.27520.1741-0.12120.1126-0.23450.01780.0248-0.07680.08510.0581182.996192.37197.622
154.466-5.30830.43151.21860.89671.89780.2069-0.07650.13040.2391-0.11520.56010.025-0.0655-0.0917-0.24350.02350.0174-0.0873-0.0349-0.1163165.06192.248195.687
164.78244.1044-1.03262.85753.08570-0.02470.1263-0.2950.18240.07010.5654-0.0717-0.5158-0.0454-0.0630.02580.13420.13840.09750.2545151.462192.567197.363
173.1985-1.35430.82751.6902-0.35844.16350.0145-0.2894-0.20330.08940.15070.41770.3388-0.5513-0.1652-0.06930.0435-0.01990.0173-0.06490.0526160.941190.117195.826
184.0999-4.7582-1.3441.8494-5.42980.6617-0.0994-0.9441-0.60820.42680.39271.22280.2039-0.4859-0.2933-0.1019-0.04150.25280.11130.15930.1505162.733182.393205.468
1917.2265.0510.26662.15741.12261.56230.3555-1.04690.39910.17350.0899-0.1137-0.49430.1664-0.4454-0.11050.0063-0.0572-0.2373-0.0705-0.1912185.938194.636203.264
201.5452-0.17778.539807.67492.81970.0852-0.13610.2180.5052-0.1173-0.8445-0.39730.60130.0321-0.0002-0.2097-0.21920.24950.05540.1818197.232197.739207.539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|26 - 41}
2X-RAY DIFFRACTION2{A|42 - 75}
3X-RAY DIFFRACTION3{A|76 - 96}
4X-RAY DIFFRACTION4{A|97 - 107}
5X-RAY DIFFRACTION5{B|137 - 162}
6X-RAY DIFFRACTION6{B|163 - 190}
7X-RAY DIFFRACTION7{B|191 - 205}
8X-RAY DIFFRACTION8{B|206 - 218}
9X-RAY DIFFRACTION9{B|219 - 236}
10X-RAY DIFFRACTION10{B|237 - 270}
11X-RAY DIFFRACTION11{B|271 - 314}
12X-RAY DIFFRACTION12{B|315 - 338}
13X-RAY DIFFRACTION13{B|339 - 392}
14X-RAY DIFFRACTION14{B|393 - 401}
15X-RAY DIFFRACTION15{B|402 - 426}
16X-RAY DIFFRACTION16{B|427 - 434}
17X-RAY DIFFRACTION17{B|435 - 459}
18X-RAY DIFFRACTION18{B|460 - 472}
19X-RAY DIFFRACTION19{B|473 - 493}
20X-RAY DIFFRACTION20{B|494 - 509}

+
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