[English] 日本語
Yorodumi
- PDB-4nhh: Structure of 2G12 IgG Dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nhh
TitleStructure of 2G12 IgG Dimer
Components
  • 2G12 IgG dimer heavy chain
  • 2G12 IgG dimer light chain
  • Hepatitis B virus receptor binding protein
KeywordsIMMUNE SYSTEM / Ig / antibody
Function / homology
Function and homology information


immunoglobulin complex / plasma membrane
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Hepatitis B virus receptor binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.5 Å
AuthorsWu, Y. / West Jr., A.P. / Kim, H.J. / Thornton, M.E. / Ward, A.B. / Bjorkman, P.J.
CitationJournal: Cell Rep / Year: 2013
Title: Structural basis for enhanced HIV-1 neutralization by a dimeric immunoglobulin G form of the glycan-recognizing antibody 2G12.
Authors: Wu, Y. / West, A.P. / Kim, H.J. / Thornton, M.E. / Ward, A.B. / Bjorkman, P.J.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: 2G12 IgG dimer light chain
H: Hepatitis B virus receptor binding protein
K: 2G12 IgG dimer light chain
M: Hepatitis B virus receptor binding protein
A: 2G12 IgG dimer heavy chain
B: 2G12 IgG dimer heavy chain
G: 2G12 IgG dimer light chain
E: Hepatitis B virus receptor binding protein
F: 2G12 IgG dimer light chain
I: Hepatitis B virus receptor binding protein
C: 2G12 IgG dimer heavy chain
D: 2G12 IgG dimer heavy chain
Q: 2G12 IgG dimer light chain
O: Hepatitis B virus receptor binding protein
P: 2G12 IgG dimer light chain
R: Hepatitis B virus receptor binding protein
J: 2G12 IgG dimer heavy chain
N: 2G12 IgG dimer heavy chain


Theoretical massNumber of molelcules
Total (without water)428,57718
Polymers428,57718
Non-polymers00
Water0
1
L: 2G12 IgG dimer light chain
H: Hepatitis B virus receptor binding protein
K: 2G12 IgG dimer light chain
M: Hepatitis B virus receptor binding protein
A: 2G12 IgG dimer heavy chain
B: 2G12 IgG dimer heavy chain
G: 2G12 IgG dimer light chain
E: Hepatitis B virus receptor binding protein
F: 2G12 IgG dimer light chain
I: Hepatitis B virus receptor binding protein
C: 2G12 IgG dimer heavy chain
D: 2G12 IgG dimer heavy chain


Theoretical massNumber of molelcules
Total (without water)285,71812
Polymers285,71812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Q: 2G12 IgG dimer light chain
O: Hepatitis B virus receptor binding protein
P: 2G12 IgG dimer light chain
R: Hepatitis B virus receptor binding protein
J: 2G12 IgG dimer heavy chain
N: 2G12 IgG dimer heavy chain

Q: 2G12 IgG dimer light chain
O: Hepatitis B virus receptor binding protein
P: 2G12 IgG dimer light chain
R: Hepatitis B virus receptor binding protein
J: 2G12 IgG dimer heavy chain
N: 2G12 IgG dimer heavy chain


Theoretical massNumber of molelcules
Total (without water)285,71812
Polymers285,71812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)374.731, 374.731, 64.455
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain L and (resseq 2:212 )
21chain K and (resseq 2:212 )
31chain G and (resseq 2:212 )
41chain F and (resseq 2:212 )
51chain Q and (resseq 2:212 )
61chain P and (resseq 2:212 )
12chain A and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
22chain B and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
32chain C and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
42chain D and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
52chain J and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
62chain N and (resseq 238:285 or resseq 287:292 or resseq 301:443 )
13chain H and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )
23chain M and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )
33chain E and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )
43chain I and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )
53chain O and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )
63chain R and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain L and (resseq 2:212 )L2 - 212
211chain K and (resseq 2:212 )K2 - 212
311chain G and (resseq 2:212 )G2 - 212
411chain F and (resseq 2:212 )F2 - 212
511chain Q and (resseq 2:212 )Q2 - 212
611chain P and (resseq 2:212 )P2 - 212
112chain A and (resseq 238:285 or resseq 287:292 or resseq 301:443 )A238 - 285
122chain A and (resseq 238:285 or resseq 287:292 or resseq 301:443 )A287 - 292
132chain A and (resseq 238:285 or resseq 287:292 or resseq 301:443 )A301 - 443
212chain B and (resseq 238:285 or resseq 287:292 or resseq 301:443 )B238 - 285
222chain B and (resseq 238:285 or resseq 287:292 or resseq 301:443 )B287 - 292
232chain B and (resseq 238:285 or resseq 287:292 or resseq 301:443 )B301 - 443
312chain C and (resseq 238:285 or resseq 287:292 or resseq 301:443 )C238 - 285
322chain C and (resseq 238:285 or resseq 287:292 or resseq 301:443 )C287 - 292
332chain C and (resseq 238:285 or resseq 287:292 or resseq 301:443 )C301 - 443
412chain D and (resseq 238:285 or resseq 287:292 or resseq 301:443 )D238 - 285
422chain D and (resseq 238:285 or resseq 287:292 or resseq 301:443 )D287 - 292
432chain D and (resseq 238:285 or resseq 287:292 or resseq 301:443 )D301 - 443
512chain J and (resseq 238:285 or resseq 287:292 or resseq 301:443 )J238 - 285
522chain J and (resseq 238:285 or resseq 287:292 or resseq 301:443 )J287 - 292
532chain J and (resseq 238:285 or resseq 287:292 or resseq 301:443 )J301 - 443
612chain N and (resseq 238:285 or resseq 287:292 or resseq 301:443 )N238 - 285
622chain N and (resseq 238:285 or resseq 287:292 or resseq 301:443 )N287 - 292
632chain N and (resseq 238:285 or resseq 287:292 or resseq 301:443 )N301 - 443
113chain H and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )H1 - 129
123chain H and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )H130 - 154
133chain H and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )H159 - 180
143chain H and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )H169 - 200
153chain H and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )H189 - 222
213chain M and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )M1 - 127
223chain M and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )M136 - 154
233chain M and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )M171 - 180
243chain M and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )M182 - 200
253chain M and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )M205 - 222
313chain E and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )E1 - 129
323chain E and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )E130 - 154
333chain E and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )E159 - 180
343chain E and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )E169 - 200
353chain E and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )E189 - 222
413chain I and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )I1 - 127
423chain I and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )I130 - 154
433chain I and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )I159 - 180
443chain I and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )I169 - 200
453chain I and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )I189 - 222
513chain O and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )O1 - 127
523chain O and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )O136 - 154
533chain O and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )O171 - 180
543chain O and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )O182 - 200
553chain O and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )O205 - 222
613chain R and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )R1 - 127
623chain R and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )R136 - 154
633chain R and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )R171 - 180
643chain R and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )R182 - 200
653chain R and (resseq 1:127 or resseq 136:154 or resseq 171:180 or resseq 182:200 or resseq 205:222 )R205 - 222

NCS ensembles :
ID
1
2
3

-
Components

#1: Antibody
2G12 IgG dimer light chain


Mass: 23233.904 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein
Hepatitis B virus receptor binding protein


Mass: 24248.408 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PYX1
#3: Protein
2G12 IgG dimer heavy chain


Mass: 23947.131 Da / Num. of mol.: 6 / Fragment: unp residues 139-348
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PYX1*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% Tascimate, 10% PEGMME5000, 100 mM HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 6→65 Å / Num. all: 10665 / Num. obs: 10665

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.5→64.905 Å / SU ML: 1.28 / σ(F): 1.99 / Phase error: 47.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3657 511 4.83 %
Rwork0.3813 --
obs0.3805 10576 98.93 %
all-113124 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 6.5→64.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28972 0 0 0 28972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03729683
X-RAY DIFFRACTIONf_angle_d1.78240278
X-RAY DIFFRACTIONf_dihedral_angle_d15.92410712
X-RAY DIFFRACTIONf_chiral_restr0.14563
X-RAY DIFFRACTIONf_plane_restr0.0155117
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11L1619X-RAY DIFFRACTIONPOSITIONAL0.803
12K1619X-RAY DIFFRACTIONPOSITIONAL0.803
13G1619X-RAY DIFFRACTIONPOSITIONAL0.001
14F1619X-RAY DIFFRACTIONPOSITIONAL0.803
15Q1619X-RAY DIFFRACTIONPOSITIONAL0.001
16P1619X-RAY DIFFRACTIONPOSITIONAL0.803
21A1574X-RAY DIFFRACTIONPOSITIONAL1.25
22B1574X-RAY DIFFRACTIONPOSITIONAL1.25
23C1575X-RAY DIFFRACTIONPOSITIONAL0.001
24D1574X-RAY DIFFRACTIONPOSITIONAL1.25
25J1575X-RAY DIFFRACTIONPOSITIONAL0.001
26N1574X-RAY DIFFRACTIONPOSITIONAL1.25
31H1433X-RAY DIFFRACTIONPOSITIONAL0.797
32M1433X-RAY DIFFRACTIONPOSITIONAL0.797
33E1456X-RAY DIFFRACTIONPOSITIONAL0.001
34I1435X-RAY DIFFRACTIONPOSITIONAL0.796
35O1446X-RAY DIFFRACTIONPOSITIONAL0.001
36R1433X-RAY DIFFRACTIONPOSITIONAL0.797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.5004-7.15380.42911460.41822463X-RAY DIFFRACTION99
7.1538-8.18730.40481180.42862479X-RAY DIFFRACTION99
8.1873-10.30840.3441120.35982524X-RAY DIFFRACTION99
10.3084-64.90850.34331350.36562599X-RAY DIFFRACTION98

+
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