[English] 日本語
Yorodumi
- PDB-7lr4: Complex of Fab 2/1.12 with domain 3 of P. berghei HAP2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lr4
TitleComplex of Fab 2/1.12 with domain 3 of P. berghei HAP2
Components
  • (D3_2/1.12 Fab ...) x 2
  • Hapless 2
KeywordsCELL ADHESION/IMMUNE SYSTEM / transmission-blocking malaria vaccine / membrane fusion / gamete fusogen / monoclonal antibody / SURFACTANT PROTEIN / CELL ADHESION / CELL ADHESION-IMMUNE SYSTEM complex
Function / homologyHAP2/GCS1 / fusion of sperm to egg plasma membrane involved in single fertilization / fertilization / plasma membrane => GO:0005886 / lipid binding / plasma membrane / Hapless 2
Function and homology information
Biological speciesMus musculus (house mouse)
Plasmodium berghei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFeng, J. / Dong, X.C. / Su, Y. / Lu, X.F. / Springer, T.A.
CitationJournal: Elife / Year: 2021
Title: Structural basis of malaria transmission blockade by a monoclonal antibody to gamete fusogen HAP2.
Authors: Feng, J. / Dong, X. / DeCosta, A. / Su, Y. / Angrisano, F. / Sala, K.A. / Blagborough, A.M. / Lu, C. / Springer, T.A.
History
DepositionFeb 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: 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 / _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
H: D3_2/1.12 Fab heavy chain
L: D3_2/1.12 Fab light chain
A: D3_2/1.12 Fab heavy chain
B: D3_2/1.12 Fab light chain
C: Hapless 2
D: Hapless 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,41313
Polymers123,6426
Non-polymers7727
Water6,377354
1
H: D3_2/1.12 Fab heavy chain
L: D3_2/1.12 Fab light chain
D: Hapless 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2086
Polymers61,8213
Non-polymers3873
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-81 kcal/mol
Surface area24680 Å2
MethodPISA
2
A: D3_2/1.12 Fab heavy chain
B: D3_2/1.12 Fab light chain
C: Hapless 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2057
Polymers61,8213
Non-polymers3844
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-70 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.880, 187.100, 74.370
Angle α, β, γ (deg.)90.00, 95.81, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules CD

#3: Protein Hapless 2 / Generative cell specific-1


Mass: 13865.662 Da / Num. of mol.: 2 / Mutation: N516T, S533N, N539Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (eukaryote) / Gene: HAP2, GCS1, PB000710.01.0 / Production host: Homo sapiens (human) / References: UniProt: Q4YCF6

-
Antibody , 2 types, 4 molecules HALB

#1: Antibody D3_2/1.12 Fab heavy chain


Mass: 24236.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody D3_2/1.12 Fab light chain


Mass: 23719.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

-
Non-polymers , 3 types, 361 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 25% PEG3350, 0.2M Ammonium Sulfate, 0.1M Bis-Tris pH5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 68138 / % possible obs: 98.4 % / Redundancy: 3.55 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.42
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.69 % / Rmerge(I) obs: 1.53 / Mean I/σ(I) obs: 0.52 / Num. unique obs: 4935 / CC1/2: 0.109 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XSCALEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A6D

2a6d


Resolution: 2.1→47.685 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.04
RfactorNum. reflection% reflection
Rfree0.2309 2000 2.94 %
Rwork0.1887 --
obs0.1899 68128 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→47.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8151 0 42 354 8547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038425
X-RAY DIFFRACTIONf_angle_d0.55611489
X-RAY DIFFRACTIONf_dihedral_angle_d8.9735018
X-RAY DIFFRACTIONf_chiral_restr0.0441307
X-RAY DIFFRACTIONf_plane_restr0.0031451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.15260.39281400.37014612X-RAY DIFFRACTION97
2.1526-2.21080.36981420.33984729X-RAY DIFFRACTION98
2.2108-2.27580.35271430.31614694X-RAY DIFFRACTION98
2.2758-2.34930.33351420.3084689X-RAY DIFFRACTION98
2.3493-2.43320.36021430.31374770X-RAY DIFFRACTION98
2.4332-2.53070.36131410.29194656X-RAY DIFFRACTION98
2.5307-2.64580.33571430.26464715X-RAY DIFFRACTION98
2.6458-2.78530.28791430.24064727X-RAY DIFFRACTION98
2.7853-2.95980.28421430.22694765X-RAY DIFFRACTION99
2.9598-3.18830.27611440.20594723X-RAY DIFFRACTION99
3.1883-3.5090.23161420.18514729X-RAY DIFFRACTION99
3.509-4.01660.22021440.16044746X-RAY DIFFRACTION98
4.0166-5.05960.14641440.12134751X-RAY DIFFRACTION99
5.0596-47.6850.17671460.15064822X-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)
11.0153-0.0675-0.18083.1559-1.47343.42240.1183-0.0357-0.09250.1206-0.2764-0.26950.25020.3320.14140.59490.0672-0.12750.4814-0.04260.4545.06432.666-2.516
21.25931.99961.40874.93821.04612.66980.2496-0.1128-0.0590.5924-0.48440.34720.8141-0.32140.26020.7399-0.00560.15480.5043-0.10170.6508-11.8324.059-3.416
31.42281.7147-0.69735.15310.28391.1977-0.0780.3631-0.0177-0.8519-0.03760.6834-0.1434-0.22740.10790.76580.181-0.23180.5188-0.08410.5402-7.64230.08-21.394
43.03310.72270.89992.93640.82386.5983-0.0948-0.84940.40830.4588-0.82931.4176-0.0675-1.58220.57470.6717-0.09140.2090.9715-0.53541.2673-27.9937.784-5.952
56.5866-0.09721.81118.1651-0.59548.5093-0.1695-0.44890.50780.9730.1739-0.3426-0.32360.4652-0.04380.54270.0549-0.13240.5425-0.00350.44810.74254.096-15.9
66.4640.69960.18946.22960.56537.61810.01750.3392-0.5593-0.1310.0008-0.80491.06490.0855-0.02340.66090.0623-0.04940.46890.08270.56213.993-61.087-18.56
71.25780.27040.78773.418-0.78324.33720.07940.0622-0.13990.12660.0194-0.37110.01530.1984-0.07510.3137-0.0085-0.03520.45240.00460.401610.768-39.245-32.644
86.8202-1.7696-4.76044.60582.21147.30040.4256-0.16910.89320.0287-0.11250.1513-0.49160.2346-0.27490.3716-0.08170.05610.40540.01520.5085-8.882-8.664-37.591
93.8761-3.1697-1.44725.58571.7412.1566-0.1195-0.1718-0.30840.6088-0.03790.27930.3565-0.3290.18850.5046-0.0822-0.00080.49180.06060.3714-4.246-40.394-16.959
105.05550.2226-0.6313.5515-2.888.08860.02230.73860.7472-0.29020.1740.2835-0.0249-0.2997-0.20570.3253-0.03230.03920.41020.0710.4841-22.72-16.222-37.874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:108 )A2 - 108
2X-RAY DIFFRACTION2( CHAIN A AND RESID 109:213 )A109 - 213
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1:119 )B1 - 119
4X-RAY DIFFRACTION4( CHAIN B AND RESID 120:212 )B120 - 212
5X-RAY DIFFRACTION5( CHAIN C AND RESID 502:613 )C502 - 613
6X-RAY DIFFRACTION6( CHAIN D AND RESID 502:612 )D502 - 612
7X-RAY DIFFRACTION7( CHAIN H AND RESID 1:119 )H1 - 119
8X-RAY DIFFRACTION8( CHAIN H AND RESID 120:221 )H120 - 221
9X-RAY DIFFRACTION9( CHAIN L AND RESID 1:108 )L1 - 108
10X-RAY DIFFRACTION10( CHAIN L AND RESID 109:213 )L109 - 213

+
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