[English] 日本語
Yorodumi
- PDB-7jrd: The crystal structure of lactoferrin binding protein B (LbpB) fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jrd
TitleThe crystal structure of lactoferrin binding protein B (LbpB) from Neisseria meningitidis in complex with human lactoferrin
Components
  • Lactoferrin-binding protein B
  • Lactotransferrin
KeywordsMETAL TRANSPORT / Lactoferrin binding protein B / Neisseria / iron scavenging / lactoferrin / TRANSPORT PROTEIN
Function / homology
Function and homology information


antifungal humoral response / : / monoatomic ion transport / regulation of cytokine production / ossification / cell outer membrane / antibacterial humoral response / iron ion binding / serine-type endopeptidase activity / cell surface / extracellular space
Similarity search - Function
Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / Transferrin-binding protein B, N-lobe handle / TbpB, N-lobe handle domain superfamily / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Lactotransferrin / Transferrin-like domain signature 2. ...Transferrin-binding protein B, C-lobe handle domain / TbpB, C-lobe handle domain superfamily / C-lobe handle domain of Tf-binding protein B / Transferrin-binding protein B, N-lobe handle / TbpB, N-lobe handle domain superfamily / N-Lobe handle Tf-binding protein B / Transferrin-binding protein B, C-lobe/N-lobe beta barrel domain / C-lobe and N-lobe beta barrels of Tf-binding protein B / Lactotransferrin / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
BICARBONATE ION / : / Transferrin-binding protein B / Lactotransferrin
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsYadav, R. / Noinaj, N.
CitationJournal: Elife / Year: 2021
Title: Structural insight into the dual function of LbpB in mediating Neisserial pathogenesis.
Authors: Ravi Yadav / Srinivas Govindan / Courtney Daczkowski / Andrew Mesecar / Srinivas Chakravarthy / Nicholas Noinaj /
Abstract: Lactoferrin-binding protein B (LbpB) is a lipoprotein present on the surface of that has been postulated to serve dual functions during pathogenesis in both iron acquisition from lactoferrin (Lf), ...Lactoferrin-binding protein B (LbpB) is a lipoprotein present on the surface of that has been postulated to serve dual functions during pathogenesis in both iron acquisition from lactoferrin (Lf), and in providing protection against the cationic antimicrobial peptide lactoferricin (Lfcn). While previous studies support a dual role for LbpB, exactly how these ligands interact with LbpB has remained unknown. Here, we present the structures of LbpB from and in complex with human holo-Lf, forming a 1:1 complex and confirmed by size-exclusion chromatography small-angle X-ray scattering. LbpB consists of N- and C-lobes with the N-lobe interacting extensively with the C-lobe of Lf. Our structures provide insight into LbpB's preference towards holo-Lf, and our mutagenesis and binding studies show that Lf and Lfcn bind independently. Our studies provide the molecular details for how LbpB serves to capture and preserve Lf in an iron-bound state for delivery to the membrane transporter LbpA for iron piracy, and as an antimicrobial peptide sink to evade host immune defenses.
History
DepositionAug 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lactoferrin-binding protein B
B: Lactotransferrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,47919
Polymers155,9962
Non-polymers1,48317
Water23413
1
B: Lactotransferrin
hetero molecules

A: Lactoferrin-binding protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,47919
Polymers155,9962
Non-polymers1,48317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_557x+1/2,-y+1/2,-z+9/41
Buried area4680 Å2
ΔGint-172 kcal/mol
Surface area52800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.388, 120.388, 207.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Lactoferrin-binding protein B


Mass: 79562.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: MC58 / Gene: lbpB, NMB1541 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9JYK4
#2: Protein Lactotransferrin


Mass: 76434.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Oryza sativa (Asian cultivated rice) / References: UniProt: W8QEY1

-
Non-polymers , 4 types, 30 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: CHO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.3 M ammonium sulphate, 60 mM Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 36195 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.985 / Rpim(I) all: 0.091 / Net I/σ(I): 14
Reflection shellResolution: 2.85→2.95 Å / Mean I/σ(I) obs: 1.33 / Num. unique obs: 3547 / CC1/2: 0.405 / Rpim(I) all: 1.022

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U9C, 2BJJ

4u9c

2bjj


Resolution: 2.85→47.78 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 2000 5.53 %
Rwork0.2009 34135 -
obs0.2036 36135 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 309.93 Å2 / Biso mean: 87.6896 Å2 / Biso min: 36.84 Å2
Refinement stepCycle: final / Resolution: 2.85→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9448 0 1853 13 11314
Biso mean--134.21 60.17 -
Num. residues----998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029714
X-RAY DIFFRACTIONf_angle_d0.55913169
X-RAY DIFFRACTIONf_dihedral_angle_d20.4373470
X-RAY DIFFRACTIONf_chiral_restr0.0411425
X-RAY DIFFRACTIONf_plane_restr0.0041740
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.930.46231390.35592369250899
2.93-30.36491400.310723892529100
3-3.090.33221400.274323992539100
3.09-3.190.27681400.25923852525100
3.19-3.310.26011410.25123962537100
3.31-3.440.26741410.236124262567100
3.44-3.60.29761420.210123982540100
3.6-3.790.24441420.195224362578100
3.79-4.020.23761410.176824202561100
4.02-4.330.24851440.166124462590100
4.33-4.770.19051430.151724392582100
4.77-5.460.20161450.170324802625100
5.46-6.870.25681470.206925052652100
6.87-47.780.24531550.198926472802100
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)
17.831-2.8376-0.08895.69540.03062.5216-0.067-0.44350.15310.1667-0.1166-0.2004-0.2004-0.01670.07430.3905-0.08-0.00270.44180.08510.3832-32.340834.875235.9234
28.894-4.1687-1.14592.74571.75511.9131-0.3746-0.8344-0.37850.52880.55210.004-0.1950.1325-0.27860.5481-0.0051-0.04660.73410.04240.4043-30.377840.5943233.6702
39.5112-3.95482.20933.4605-2.28696.7325-0.01830.25621.6439-0.1669-0.2648-0.4256-0.91720.67730.26830.7284-0.11580.13980.43690.04140.601-29.88952.7446221.9803
48.8721-1.9179-0.924.40670.02461.33820.0245-0.43440.28990.41-0.1923-0.5840.17210.19040.17450.4660.00520.03630.445-0.07140.4588-20.16438.3912234.5964
51.9773-2.1876-0.8488.28420.63635.07870.25570.79890.4576-0.6252-0.23730.138-0.3946-0.48870.02640.31420.0160.07820.66140.10070.6271-47.019250.0742218.5921
68.2379-1.08062.08832.7737-1.5914.21360.19720.0802-0.5725-0.2842-0.3235-0.45550.55760.01990.03260.4543-0.00380.09440.41360.03140.4262-24.964534.2183218.3234
73.10750.0128-0.31763.1427-0.07522.70590.01940.621-0.0675-0.2544-0.03990.05710.0043-0.37590.03140.3999-0.0454-0.0220.6194-0.03010.4458-42.645439.9922215.4444
86.8943-2.31421.0155.2741-6.15217.68850.51221.33090.0468-3.46040.32373.25481.3749-0.903-0.46721.73440.1154-0.65281.14790.1251.6741-64.091858.4866214.7837
96.7103-5.4873-2.71765.15650.30618.88270.5864-0.57450.6789-0.3017-0.0274-0.0256-0.57560.2751-0.63440.5449-0.02860.20550.9088-0.09881.0867-53.533760.3164237.3051
102.81680.50714.24112.60692.61427.78470.1577-1.77010.67180.50030.0221-0.116-0.0732-0.4041-0.120.97250.17010.14061.365-0.21321.0427-56.519158.7347246.5867
110.63540.1532-1.62683.78171.25495.80020.1487-0.18560.04620.3274-0.3041-0.25430.18060.40410.18560.60640.0677-0.09131.0597-0.14261.2486-63.015965.3056240.9128
128.2476-0.90534.2145.9171-0.46823.44140.2894-0.52650.9272-0.5055-0.95260.4562-0.4315-1.42880.3860.77740.24580.02611.1595-0.14421.2107-75.392868.9561236.1382
132.17370.86930.5770.34870.57413.58690.28050.55740.0055-0.5397-0.85560.736-1.0758-0.1370.71221.26040.46450.01481.0117-0.03681.0667-69.418377.4366238.3834
143.56175.92740.26979.77890.29442.0993-0.75510.7675-1.9449-0.20750.2752-0.5401-0.92270.17110.29321.36770.1356-0.14661.5674-0.36541.5368-69.036361.2278233.16
151.87332.0216-1.70582.157-2.1465.2759-0.34370.4910.09851.19220.65040.4426-1.2754-0.3561-0.11970.92490.1339-0.01111.1322-0.2271.3774-63.591970.9338232.1967
162.1017-0.4526-0.02613.4884-1.27053.1741-0.0869-0.24890.30850.25330.0127-0.5467-0.30220.3340.06950.4897-0.01440.01190.5251-0.14890.563415.057461.9376245.7244
174.68270.7753-0.19673.8348-1.54523.65530.01210.091-0.10040.0059-0.06660.04110.0406-0.19650.04250.36960.00070.01710.3363-0.06550.37690.589536.4709226.9581
181.8806-0.1770.46911.8835-0.17242.7430.01020.36610.0256-0.31770.0485-0.0576-0.00370.1175-0.04710.388-0.01530.06850.4332-0.00140.4003-4.00539.3178206.0691
192.66010.5377-0.90137.244-1.95113.2484-0.04310.38540.0761-0.335-0.0064-0.32990.13770.2450.00690.39640.0962-0.01030.6381-0.02080.36954.426136.4274217.762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 67 )A36 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 106 )A68 - 106
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 134 )A107 - 134
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 166 )A135 - 166
5X-RAY DIFFRACTION5chain 'A' and (resid 167 through 189 )A167 - 189
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 231 )A190 - 231
7X-RAY DIFFRACTION7chain 'A' and (resid 232 through 343 )A232 - 343
8X-RAY DIFFRACTION8chain 'A' and (resid 352 through 364 )A352 - 364
9X-RAY DIFFRACTION9chain 'A' and (resid 365 through 405 )A365 - 405
10X-RAY DIFFRACTION10chain 'A' and (resid 406 through 441 )A406 - 441
11X-RAY DIFFRACTION11chain 'A' and (resid 442 through 569 )A442 - 569
12X-RAY DIFFRACTION12chain 'A' and (resid 570 through 612 )A570 - 612
13X-RAY DIFFRACTION13chain 'A' and (resid 613 through 650 )A613 - 650
14X-RAY DIFFRACTION14chain 'A' and (resid 651 through 662 )A651 - 662
15X-RAY DIFFRACTION15chain 'A' and (resid 663 through 713 )A663 - 713
16X-RAY DIFFRACTION16chain 'B' and (resid 5 through 333 )B5 - 333
17X-RAY DIFFRACTION17chain 'B' and (resid 334 through 425 )B334 - 425
18X-RAY DIFFRACTION18chain 'B' and (resid 426 through 621 )B426 - 621
19X-RAY DIFFRACTION19chain 'B' and (resid 622 through 692 )B622 - 692

+
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