[English] 日本語
Yorodumi
- PDB-7rpt: Crystal Structure of Protective Human Antibody 3A6 Fab Against Eb... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rpt
TitleCrystal Structure of Protective Human Antibody 3A6 Fab Against Ebola Virus
Components
  • 3A6 Fab heavy chain
  • 3A6 Fab light chain
KeywordsANTIVIRAL PROTEIN / Antibody
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSalie, Z.L. / Saphire, E.O. / Davis, C.W. / Ahmed, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States) United States
CitationJournal: To Be Published
Title: Protection against Ebola virus disease and neutralization mechanism of a survivor's anti-stalk/MPER antibody
Authors: Salie, Z.L. / Saphire, E.O.
History
DepositionAug 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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: 3A6 Fab heavy chain
B: 3A6 Fab light chain
C: 3A6 Fab heavy chain
D: 3A6 Fab light chain
E: 3A6 Fab heavy chain
F: 3A6 Fab light chain
G: 3A6 Fab heavy chain
H: 3A6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)188,1798
Polymers188,1798
Non-polymers00
Water3,855214
1
A: 3A6 Fab heavy chain
B: 3A6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,0452
Polymers47,0452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 3A6 Fab heavy chain
D: 3A6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,0452
Polymers47,0452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 3A6 Fab heavy chain
F: 3A6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,0452
Polymers47,0452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: 3A6 Fab heavy chain
H: 3A6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,0452
Polymers47,0452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.659, 65.674, 125.556
Angle α, β, γ (deg.)98.737, 91.366, 96.009
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 18 or resid 20...
d_2ens_1(chain "C" and (resid 1 through 18 or resid 20...
d_3ens_1(chain "E" and (resid 1 through 18 or resid 20...
d_4ens_1(chain "G" and (resid 1 through 18 or resid 20...
d_1ens_2(chain "B" and (resid 1 through 217 or (resid 218...
d_2ens_2(chain "D" and (resid 1 through 217 or (resid 218...
d_3ens_2(chain "F" and (resid 1 through 217 or (resid 218...
d_4ens_2chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLULEUA1 - 18
d_12ens_1LEULEUA21
d_13ens_1CYSLEUA24 - 88
d_14ens_1ASPALAA92 - 95
d_15ens_1TYRSERA98 - 118
d_16ens_1ALAPROA120 - 125
d_17ens_1VALGLYA127 - 141
d_18ens_1LEUTYRA143 - 178
d_19ens_1LEULEUA180
d_110ens_1SERILEA183 - 198
d_111ens_1ASNLYSA200 - 217
d_21ens_1GLULEUC1 - 18
d_22ens_1LEULEUC21
d_23ens_1CYSLEUC24 - 88
d_24ens_1ASPALAC92 - 95
d_25ens_1TYRSERC97 - 117
d_26ens_1ALAPROC120 - 125
d_27ens_1VALGLYC128 - 142
d_28ens_1LEUTYRC144 - 179
d_29ens_1LEULEUC181
d_210ens_1SERILEC183 - 198
d_211ens_1ASNLYSC200 - 217
d_31ens_1GLULEUE1 - 18
d_32ens_1LEULEUE21
d_33ens_1CYSLEUE24 - 88
d_34ens_1ASPALAE92 - 95
d_35ens_1TYRSERE98 - 118
d_36ens_1ALAPROE120 - 125
d_37ens_1VALGLYE128 - 142
d_38ens_1LEUTYRE144 - 179
d_39ens_1LEULEUE182
d_310ens_1SERILEE184 - 199
d_311ens_1ASNLYSE201 - 218
d_41ens_1GLULEUG1 - 18
d_42ens_1LEULEUG21
d_43ens_1CYSLEUG24 - 88
d_44ens_1ASPALAG94 - 97
d_45ens_1TYRSERG100 - 120
d_46ens_1ALAPROG122 - 127
d_47ens_1VALGLYG129 - 143
d_48ens_1LEUTYRG147 - 182
d_49ens_1LEULEUG185
d_410ens_1SERILEG188 - 203
d_411ens_1ASNLYSG207 - 224
d_11ens_2ASPGLUB1 - 218
d_21ens_2ASPGLUD1 - 218
d_31ens_2ASPGLUF1 - 218
d_41ens_2ASPGLUH1 - 218

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999953470224, 0.00756471020315, -0.00598602923115), (0.00323885461003, -0.321232917115, -0.946994679384), (-0.00908664994533, -0.946970003813, 0.321193469223)-39.0114701264, -5.28922070846, 41.8774808598
2given(0.972166210955, 0.207312866584, 0.109152341364), (0.207084709777, -0.978229210125, 0.0135475250266), (0.109584584924, 0.00943333486001, -0.993932709463)3.61305919038, -32.3902028448, -6.17570820918
3given(-0.986165775283, -0.12239265315, -0.111790438387), (-0.145308798994, 0.313780043971, 0.938310948961), (-0.0797647578504, 0.94157427878, -0.327223869766)-36.9211523335, -53.3043650465, 72.1223645133
4given(-0.999897680917, -0.000431672768969, 0.0142982990741), (-0.0132801669558, -0.343474478842, -0.939068112306), (0.00531647095508, -0.939161911516, 0.343433602162)-39.4122245132, -6.11069139755, 42.1962682996
5given(0.971327220451, 0.207552745607, 0.115953820992), (0.208997341666, -0.977916160412, -0.000307216219027), (0.113329351839, 0.0245324478193, -0.993254558014)3.56492293667, -32.0920014454, -5.68633055525
6given(-0.981377313923, -0.138946301796, -0.132636695281), (-0.170921367272, 0.316531421802, 0.933056131871), (-0.0876610171511, 0.938350565742, -0.33438564838)-36.7471451563, -53.744266801, 71.8480591312

-
Components

#1: Antibody
3A6 Fab heavy chain


Mass: 23047.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
3A6 Fab light chain


Mass: 23996.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG400, 0.1M HEPES:NaOH, pH7.5 and 0.2M Calcium Chloride

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.5→123.998 Å / Num. obs: 38276 / % possible obs: 78.1 % / Redundancy: 1.7 % / Biso Wilson estimate: 34.7 Å2 / CC1/2: 0.987 / Net I/σ(I): 2.7
Reflection shellResolution: 2.5→2.733 Å / Num. unique obs: 1915 / CC1/2: 0.525

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHASERphasing
STARANISOdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS Model

Resolution: 2.5→43.51 Å / SU ML: 0.3004 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.9143
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2541 1968 5.15 %
Rwork0.198 36222 -
obs0.2008 38190 65.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.44 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13007 0 0 214 13221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013513492
X-RAY DIFFRACTIONf_angle_d1.669818360
X-RAY DIFFRACTIONf_chiral_restr0.18132065
X-RAY DIFFRACTIONf_plane_restr0.00522370
X-RAY DIFFRACTIONf_dihedral_angle_d19.10074891
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.761137599348
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.756587436276
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.962306567625
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.10564098797
ens_2d_3BX-RAY DIFFRACTIONTorsion NCS0.985167126848
ens_2d_4BX-RAY DIFFRACTIONTorsion NCS1.25683937402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.3908170.2952229X-RAY DIFFRACTION5.97
2.57-2.640.3104220.29443X-RAY DIFFRACTION11.22
2.64-2.710.3415520.2673852X-RAY DIFFRACTION21.79
2.71-2.80.3854750.27241431X-RAY DIFFRACTION36.72
2.8-2.90.35271190.27422187X-RAY DIFFRACTION55.58
2.9-3.020.33131480.26192843X-RAY DIFFRACTION72.11
3.02-3.150.32521640.23713291X-RAY DIFFRACTION82.26
3.15-3.320.2932010.22353437X-RAY DIFFRACTION89.12
3.32-3.530.2672030.20223622X-RAY DIFFRACTION92.93
3.53-3.80.23241920.18693683X-RAY DIFFRACTION92.68
3.8-4.180.23562010.17683563X-RAY DIFFRACTION91.01
4.18-4.790.20151860.15933546X-RAY DIFFRACTION90.45
4.79-6.030.21762050.16633563X-RAY DIFFRACTION90.45
6.03-43.510.23021830.19813532X-RAY DIFFRACTION90.1

+
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