[English] 日本語
Yorodumi
- PDB-6dbs: Fusion surface structure, function, and dynamics of gamete fusoge... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dbs
TitleFusion surface structure, function, and dynamics of gamete fusogen HAP2
ComponentsHapless 2The Jewish Enquirer
KeywordsSTRUCTURAL PROTEIN / gamete fertilization / cell fusogens / Class II fusion proteins / hydrogen deuterium exchange
Function / homology
Function and homology information


fusion of sperm to egg plasma membrane involved in single fertilization / cell projection membrane / protein insertion into membrane / cytoplasmic vesicle membrane / cytoplasmic vesicle / lipid binding / plasma membrane
Similarity search - Function
Generative cell specific-1/HAP2 domain / Male gamete fusion factor / HAP2/GCS1
Similarity search - Domain/homology
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsFeng, J. / Dong, X. / Springer, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)NIH grants R01-CA31798 United States
CitationJournal: Elife / Year: 2018
Title: Fusion surface structure, function, and dynamics of gamete fusogen HAP2.
Authors: Feng, J. / Dong, X. / Pinello, J. / Zhang, J. / Lu, C. / Iacob, R.E. / Engen, J.R. / Snell, W.J. / Springer, T.A.
History
DepositionMay 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hapless 2
C: Hapless 2
B: Hapless 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,88315
Polymers179,8083
Non-polymers4,07512
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24070 Å2
ΔGint-42 kcal/mol
Surface area66440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.220, 117.600, 115.210
Angle α, β, γ (deg.)90.00, 123.79, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Hapless 2 / The Jewish Enquirer / HAP2-GCS1 / HAP2 / Generative cell specific-1


Mass: 59936.090 Da / Num. of mol.: 3 / Fragment: UNP residues 23-582
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: HAP2, GCS1 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A4GRC6
#2: 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
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% PEG3350, 0.1 M HEPES, pH 7.5, 0.35 M ammonium acetate
PH range: 7.0-7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.071951 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Mar 11, 2017 / Details: GM/CA
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071951 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 66071 / % possible obs: 97.3 % / Redundancy: 4.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/av σ(I): 9.4 / Net I/σ(I): 9.4
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.3 % / Rmerge(I) obs: 3.559 / Mean I/σ(I) obs: 0.33 / Num. unique obs: 4346 / CC1/2: 0.16 / % possible all: 85.8

-
Processing

Software
NameVersionClassification
PHENIXV1.0refinement
Blu-Ice5data collection
Coot0.8.9model building
AutoSolV1.0phasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5MF1

5mf1


Resolution: 2.602→48.995 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.19
RfactorNum. reflection% reflection
Rfree0.2757 1827 2.8 %
Rwork0.2372 --
obs0.2383 65203 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.602→48.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11615 0 265 95 11975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212173
X-RAY DIFFRACTIONf_angle_d0.52816633
X-RAY DIFFRACTIONf_dihedral_angle_d12.2147331
X-RAY DIFFRACTIONf_chiral_restr0.0391973
X-RAY DIFFRACTIONf_plane_restr0.0052113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6022-2.67260.5171120.52074135X-RAY DIFFRACTION82
2.6726-2.75120.44311490.47244670X-RAY DIFFRACTION93
2.7512-2.840.48221240.44834795X-RAY DIFFRACTION97
2.84-2.94150.42131420.40794954X-RAY DIFFRACTION97
2.9415-3.05930.46791330.37454901X-RAY DIFFRACTION99
3.0593-3.19850.48741360.36674972X-RAY DIFFRACTION98
3.1985-3.36710.38941510.33334939X-RAY DIFFRACTION98
3.3671-3.5780.31791440.28024939X-RAY DIFFRACTION98
3.578-3.85410.41131580.25134955X-RAY DIFFRACTION99
3.8541-4.24180.24871460.2264995X-RAY DIFFRACTION99
4.2418-4.85510.19311410.17875026X-RAY DIFFRACTION99
4.8551-6.1150.20961430.19295008X-RAY DIFFRACTION99
6.115-49.00330.23521480.19235087X-RAY DIFFRACTION99
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)
14.73760.63820.63321.99321.71224.05470.1480.3248-0.33380.29570.1799-0.83140.28590.6386-0.16590.64420.09210.03871.04570.08831.3624265.147548.182824.9617
26.07550.31-2.1321.4789-0.17391.86790.0745-0.4341-0.31610.2198-0.08820.35960.017-0.38820.05720.6148-0.00950.07581.00310.08591.1355209.283344.806839.2481
36.0821-3.46780.9664.06010.45542.6327-0.11940.5331-0.82380.2397-0.08140.12110.0539-0.04020.14420.708-0.06750.15360.9716-0.13561.0781230.691936.681310.565
42.05410.0684-0.36081.8744-1.7455.28640.0476-0.13370.36560.0206-0.337-0.6374-0.84110.96790.19110.7926-0.19280.19471.1266-0.00771.2639261.798274.287415.8055
55.6588-0.6496-1.38681.02170.44521.74270.1859-0.09530.10250.1927-0.03470.383-0.2426-0.3866-0.14070.7015-0.08330.21291.0431-0.07521.0741209.889770.952440.9505
67.64115.6042-0.00536.0732-1.51842.33230.0681-0.7279-0.0645-0.0798-0.1716-0.104-0.07390.16770.10070.58030.03790.03931.12680.02240.8436243.807858.122846.476
73.1844-2.2112-0.86267.76261.08731.45360.2450.24790.0191-1.0228-0.1627-0.77480.12670.2949-0.0460.74320.09360.18361.2723-0.03810.9332255.717452.8167-0.8656
86.5090.6402-1.4180.9095-0.42791.54890.14170.1524-0.020.0506-0.10870.4881-0.1112-0.4597-0.01860.64480.09150.10941.2126-0.03290.9914201.795559.489118.8092
91.1878-0.5307-3.1013.37931.16128.04340.39180.44090.6289-0.13940.08790.0658-0.242-0.3541-0.49880.57350.04270.1420.93160.15851.0666230.890980.481511.0826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 23:104 or resseq 231:312 or resseq 445:465)
2X-RAY DIFFRACTION2chain A and (resseq 105:194 or resseq 205:230 or resseq 313:444)
3X-RAY DIFFRACTION3chain A and resseq 466:588
4X-RAY DIFFRACTION4chain B and (resseq 23:104 or resseq 231:312 or resseq 445:465)
5X-RAY DIFFRACTION5chain B and (resseq 105:194 or resseq 205:230 or resseq 313:444)
6X-RAY DIFFRACTION6chain B and resseq 466:588
7X-RAY DIFFRACTION7chain C and (resseq 23:104 or resseq 231:312 or resseq 445:465)
8X-RAY DIFFRACTION8chain C and (resseq 105:194 or resseq 205:230 or resseq 313:444)
9X-RAY DIFFRACTION9chain C and resseq 466:588

+
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