[English] 日本語
Yorodumi
- PDB-5o1r: human Fab 5H2 bound to NHBA-C3 from Neisseria meningitidis serogroup B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o1r
Titlehuman Fab 5H2 bound to NHBA-C3 from Neisseria meningitidis serogroup B
Components
  • GNA2132
  • IGH@ protein
  • Uncharacterized protein
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / cell outer membrane / heparin binding / antibacterial humoral response / blood microparticle / cell adhesion / immune response ...immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / cell outer membrane / heparin binding / antibacterial humoral response / blood microparticle / cell adhesion / immune response / DNA binding / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / : / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / IGH@ protein / Neisserial heparin binding antigen
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsMalito, E. / Maritan, M.
CitationJournal: PLoS ONE / Year: 2018
Title: Structures of NHBA elucidate a broadly conserved epitope identified by a vaccine induced antibody.
Authors: Maritan, M. / Veggi, D. / Cozzi, R. / Dello Iacono, L. / Bartolini, E. / Lo Surdo, P. / Maruggi, G. / Spraggon, G. / Bottomley, M.J. / Malito, E.
History
DepositionMay 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Jan 17, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GNA2132
B: GNA2132
H: IGH@ protein
I: IGH@ protein
L: Uncharacterized protein
M: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,83711
Polymers129,5276
Non-polymers3105
Water82946
1
A: GNA2132
H: IGH@ protein
L: Uncharacterized protein
hetero molecules


  • defined by author
  • Evidence: gel filtration, the complex was isolated by gel filtration chromatography showing an elution profile compatible with the complex. The fractions corresponding to the peak were also run in ...Evidence: gel filtration, the complex was isolated by gel filtration chromatography showing an elution profile compatible with the complex. The fractions corresponding to the peak were also run in SDS-PAGE under both native and denaturant conditions, showing the presence of both the Fab and NHBA-C3
  • 64.9 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)64,8885
Polymers64,7643
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GNA2132
I: IGH@ protein
M: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9506
Polymers64,7643
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.450, 119.450, 364.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein GNA2132 / Gna2132 / Heparin binding protein / Neisserial heparin binding antigen / Putative lipoprotein GNA2132


Mass: 13706.022 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: gna2132, nhba / Variant: p20 / Plasmid: pET21b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T1R / References: UniProt: Q9JPP1
#2: Antibody IGH@ protein


Mass: 27962.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the sequence provided includes the tag which was cleaved prior to crystallization
Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6
#3: Antibody Uncharacterized protein


Mass: 23094.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q6GMX0
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS pH 8.0 and 1.6 M lithium sulphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.86→91.05 Å / Num. obs: 36688 / % possible obs: 100 % / Redundancy: 19.4 % / Biso Wilson estimate: 88.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.044 / Rrim(I) all: 0.194 / Net I/σ(I): 18.4
Reflection shellResolution: 2.86→2.93 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2628 / CC1/2: 0.557 / Rpim(I) all: 0.875 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NYX

5nyx


Resolution: 2.86→78.74 Å / Cor.coef. Fo:Fc: 0.9465 / Cor.coef. Fo:Fc free: 0.9196 / SU R Cruickshank DPI: 0.826 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.926 / SU Rfree Blow DPI: 0.301 / SU Rfree Cruickshank DPI: 0.303
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 1775 4.85 %RANDOM
Rwork0.1778 ---
obs0.1799 36573 99.95 %-
Displacement parametersBiso mean: 84.55 Å2
Baniso -1Baniso -2Baniso -3
1--7.5165 Å20 Å20 Å2
2---7.5165 Å20 Å2
3---15.0329 Å2
Refine analyzeLuzzati coordinate error obs: 0.447 Å
Refinement stepCycle: 1 / Resolution: 2.86→78.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8260 0 20 46 8326
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018499HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2911543HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2808SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes167HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1251HARMONIC5
X-RAY DIFFRACTIONt_it8499HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion21.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1108SEMIHARMONIC5
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_contact9131SEMIHARMONIC4
LS refinement shellResolution: 2.86→2.94 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2574 149 5.12 %
Rwork0.2523 2762 -
all0.2526 2911 -
obs--99.95 %
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)
16.18460.9618-0.70863.3406-0.434.5068-0.13160.2319-0.09740.12560.1619-0.04410.6718-0.1984-0.03030.0983-0.00520.0067-0.1081-0.0179-0.2994-13.533821.224833.9923
24.8081-1.5356-1.20753.17760.23583.8809-0.04210.1213-0.0397-0.0690.08770.10070.5668-0.3236-0.04560.0394-0.1424-0.0251-0.0593-0.0036-0.231320.957513.4777-10.0893
30.7081-0.09990.06061.9509-0.98442.4879-0.0223-0.01570.19460.21810.02070.0433-0.0382-0.10330.0016-0.19930.09150.02950.02680.0116-0.0851-6.071352.598310.9504
41.28840.29930.05052.21281.15663.1310.00850.04670.1525-0.05440.0255-0.12020.01190.1561-0.034-0.2513-0.01650.012-0.00550.0788-0.072527.778345.107312.8121
51.2860.1909-0.55532.7228-1.59063.6329-0.01140.22320.1332-0.33210.017-0.15630.3045-0.1268-0.0056-0.24230.09750.0160.04160.0332-0.2329-2.621343.6713-4.9052
61.29670.132-0.01962.36561.03643.4812-0.0186-0.14060.28480.3792-0.00490.0474-0.0608-0.04970.0236-0.19970.02520.0112-0.04570.0248-0.206520.601138.523128.8653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|292 - A|407 }
2X-RAY DIFFRACTION2{ B|292 - B|406 }
3X-RAY DIFFRACTION3{ H|1 - H|223 }
4X-RAY DIFFRACTION4{ I|1 - I|223 }
5X-RAY DIFFRACTION5{ L|1 - L|211 }
6X-RAY DIFFRACTION6{ M|1 - M|211 }

+
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://pdbjlc1.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