[English] 日本語
Yorodumi
- PDB-7kjh: Plasmodium falciparum protein Pf12p bound to nanobody B9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kjh
TitlePlasmodium falciparum protein Pf12p bound to nanobody B9
Components
  • Nanobody B9
  • Surface protein P12p
KeywordsUNKNOWN FUNCTION / Plasmodium falciparum / 6-cysteine protein / s48/45 domain / nanobody
Function / homology
Function and homology information


cell surface / plasma membrane
Similarity search - Function
Immunoglobulin-like - #2860 / 6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / Surface protein P12p
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDietrich, M.H. / Tham, W.H.
Funding support Australia, United Kingdom, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)GNT1154937 Australia
Wellcome Trust208693/Z/17/Z United Kingdom
CitationJournal: Biochem.J. / Year: 2021
Title: Nanobody generation and structural characterization of Plasmodium falciparum 6-cysteine protein Pf12p.
Authors: Dietrich, M.H. / Chan, L.J. / Adair, A. / Keremane, S. / Pymm, P. / Lo, A.W. / Cao, Y.C. / Tham, W.H.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nanobody B9
C: Surface protein P12p
D: Surface protein P12p
B: Nanobody B9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,76110
Polymers102,5624
Non-polymers1,1996
Water10,683593
1
A: Nanobody B9
C: Surface protein P12p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8805
Polymers51,2812
Non-polymers5993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint2 kcal/mol
Surface area17490 Å2
MethodPISA
2
D: Surface protein P12p
B: Nanobody B9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8805
Polymers51,2812
Non-polymers5993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint1 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.986, 107.044, 113.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 16 or resid 18...
21(chain B and (resid 1 through 4 or (resid 5...
12(chain C and (resid 24 through 57 or resid 59...
22(chain D and (resid 24 through 31 or (resid 32...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNGLYGLY(chain A and (resid 1 through 16 or resid 18...AA1 - 161 - 16
121LEULEUALAALA(chain A and (resid 1 through 16 or resid 18...AA18 - 7518 - 75
131LYSLYSLYSLYS(chain A and (resid 1 through 16 or resid 18...AA7676
141GLNGLNSERSER(chain A and (resid 1 through 16 or resid 18...AA1 - 1201 - 120
151GLNGLNSERSER(chain A and (resid 1 through 16 or resid 18...AA1 - 1201 - 120
161GLNGLNSERSER(chain A and (resid 1 through 16 or resid 18...AA1 - 1201 - 120
171GLNGLNSERSER(chain A and (resid 1 through 16 or resid 18...AA1 - 1201 - 120
181GLNGLNSERSER(chain A and (resid 1 through 16 or resid 18...AA1 - 1201 - 120
211GLNGLNLEULEU(chain B and (resid 1 through 4 or (resid 5...BD1 - 41 - 4
221GLNGLNGLNGLN(chain B and (resid 1 through 4 or (resid 5...BD55
231GLNGLNHOHHOH(chain B and (resid 1 through 4 or (resid 5...BD - N1 - 4011
241GLNGLNHOHHOH(chain B and (resid 1 through 4 or (resid 5...BD - N1 - 4011
251GLNGLNHOHHOH(chain B and (resid 1 through 4 or (resid 5...BD - N1 - 4011
261GLNGLNHOHHOH(chain B and (resid 1 through 4 or (resid 5...BD - N1 - 4011
112ASNASNASNASN(chain C and (resid 24 through 57 or resid 59...CB24 - 574 - 37
122VALVALPROPRO(chain C and (resid 24 through 57 or resid 59...CB59 - 7739 - 57
132ARGARGLYSLYS(chain C and (resid 24 through 57 or resid 59...CB79 - 8059 - 60
142ASNASNGLYGLY(chain C and (resid 24 through 57 or resid 59...CB82 - 10162 - 81
152SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
162SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
172SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
182SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
192SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
1102SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
1112SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
1122SERSERSERSER(chain C and (resid 24 through 57 or resid 59...CB23 - 3413 - 321
212ASNASNSERSER(chain D and (resid 24 through 31 or (resid 32...DC24 - 314 - 11
222GLUGLUGLUGLU(chain D and (resid 24 through 31 or (resid 32...DC3212
232ASNASNSERSER(chain D and (resid 24 through 31 or (resid 32...DC24 - 3414 - 321
242ASNASNSERSER(chain D and (resid 24 through 31 or (resid 32...DC24 - 3414 - 321
252ASNASNSERSER(chain D and (resid 24 through 31 or (resid 32...DC24 - 3414 - 321
262ASNASNSERSER(chain D and (resid 24 through 31 or (resid 32...DC24 - 3414 - 321

NCS ensembles :
ID
1
2

-
Components

#1: Antibody Nanobody B9


Mass: 14033.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein Surface protein P12p


Mass: 37247.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PFS12P, PF12P, PFF0620c / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C6KSX1
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#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.: 2 / Source method: obtained synthetically / 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


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG3000, 0.1 M trisodium citrate-citric acid pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953725 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 2→47.338 Å / Num. obs: 70873 / % possible obs: 100 % / Redundancy: 13.813 % / Biso Wilson estimate: 34.603 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.195 / Rrim(I) all: 0.203 / Χ2: 0.785 / Net I/σ(I): 10.73 / Num. measured all: 978968
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.1214.1261.4341.615962611311113000.7021.48799.9
2.12-2.2714.0040.9462.6914898710639106390.8390.982100
2.27-2.4513.4220.6763.84133359993799360.910.702100
2.45-2.6813.9670.4615.88128291918591850.960.479100
2.68-314.1930.2959.26117872830583050.9840.306100
3-3.4613.410.16415.6698950737973790.9940.171100
3.46-4.2313.8540.09526.4887279630063000.9980.099100
4.23-5.9613.8380.07233.6868514495149510.9990.075100
5.96-47.33812.540.0733.2236090288628780.9990.07399.7

-
Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YMO, 6WAQ

2ymo

6waq


Resolution: 2→47.338 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 2126 3 %
Rwork0.1803 68716 -
obs0.1814 70842 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.55 Å2 / Biso mean: 35.9642 Å2 / Biso min: 15.44 Å2
Refinement stepCycle: final / Resolution: 2→47.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6019 0 128 593 6740
Biso mean--66.46 41.16 -
Num. residues----767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086301
X-RAY DIFFRACTIONf_angle_d0.9328551
X-RAY DIFFRACTIONf_dihedral_angle_d6.635037
X-RAY DIFFRACTIONf_chiral_restr0.061928
X-RAY DIFFRACTIONf_plane_restr0.0051110
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A714X-RAY DIFFRACTION11.352TORSIONAL
12B714X-RAY DIFFRACTION11.352TORSIONAL
21C1472X-RAY DIFFRACTION11.352TORSIONAL
22D1472X-RAY DIFFRACTION11.352TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2-2.04650.30651390.27374492
2.0465-2.09770.31761400.24994548
2.0977-2.15440.26781400.23544527
2.1544-2.21780.27231400.21984515
2.2178-2.28940.2271410.20634552
2.2894-2.37120.26781410.21434556
2.3712-2.46620.24121390.20634499
2.4662-2.57840.2571420.2084607
2.5784-2.71430.23681410.19224538
2.7143-2.88440.2221410.18594559
2.8844-3.1070.21911410.18584575
3.107-3.41960.22081430.17064617
3.4196-3.91430.18731430.15664627
3.9143-4.93070.16921440.13384665
4.9307-47.3380.20011510.17764839

+
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