[English] 日本語
Yorodumi
- PDB-5uem: Crystal structure of 354NC37 Fab in complex with HIV-1 clade AE s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uem
TitleCrystal structure of 354NC37 Fab in complex with HIV-1 clade AE strain 93TH057 gp120
Components
  • 354NC37 Fab Heavy Chain
  • 354NC37 Fab Light Chain
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsIMMUNE SYSTEM / HIV / Envelope Protein / Antibody / Immunity
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSievers, S.A. / Gristick, H.B. / Bjorkman, P.J.
CitationJournal: Sci Transl Med / Year: 2017
Title: Coexistence of potent HIV-1 broadly neutralizing antibodies and antibody-sensitive viruses in a viremic controller.
Authors: Freund, N.T. / Wang, H. / Scharf, L. / Nogueira, L. / Horwitz, J.A. / Bar-On, Y. / Golijanin, J. / Sievers, S.A. / Sok, D. / Cai, H. / Cesar Lorenzi, J.C. / Halper-Stromberg, A. / Toth, I. / ...Authors: Freund, N.T. / Wang, H. / Scharf, L. / Nogueira, L. / Horwitz, J.A. / Bar-On, Y. / Golijanin, J. / Sievers, S.A. / Sok, D. / Cai, H. / Cesar Lorenzi, J.C. / Halper-Stromberg, A. / Toth, I. / Piechocka-Trocha, A. / Gristick, H.B. / van Gils, M.J. / Sanders, R.W. / Wang, L.X. / Seaman, M.S. / Burton, D.R. / Gazumyan, A. / Walker, B.D. / West, A.P. / Bjorkman, P.J. / Nussenzweig, M.C.
History
DepositionJan 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
H: 354NC37 Fab Heavy Chain
L: 354NC37 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,20913
Polymers88,0733
Non-polymers4,13610
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint44 kcal/mol
Surface area34740 Å2
Unit cell
Length a, b, c (Å)63.635, 67.507, 210.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules G

#1: Protein clade A/E 93TH057 HIV-1 gp120 core


Mass: 40204.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9

-
Antibody , 2 types, 2 molecules HL

#2: Antibody 354NC37 Fab Heavy Chain


Mass: 24704.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 354NC37 Fab Light Chain


Mass: 23163.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Sugars , 4 types, 9 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: 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.: 6
Source method: isolated from a genetically manipulated source
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

-
Non-polymers , 2 types, 71 molecules

#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 20% (w/v) PEG 10,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→35.743 Å / Num. obs: 27104 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.4
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.83 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7Y

3u7y


Resolution: 2.7→35.743 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2661 1431 5.57 %
Rwork0.2198 --
obs0.2223 25671 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→35.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5955 0 271 70 6296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026399
X-RAY DIFFRACTIONf_angle_d0.618754
X-RAY DIFFRACTIONf_dihedral_angle_d12.2073792
X-RAY DIFFRACTIONf_chiral_restr0.044969
X-RAY DIFFRACTIONf_plane_restr0.0041096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.79650.34421360.29142363X-RAY DIFFRACTION100
2.7965-2.90840.30841340.29032398X-RAY DIFFRACTION100
2.9084-3.04070.30461380.27292391X-RAY DIFFRACTION100
3.0407-3.20090.25791520.26192401X-RAY DIFFRACTION100
3.2009-3.40130.29641350.23242383X-RAY DIFFRACTION100
3.4013-3.66370.28611500.22132378X-RAY DIFFRACTION100
3.6637-4.03190.2761480.20052445X-RAY DIFFRACTION100
4.0319-4.61430.22381400.17532431X-RAY DIFFRACTION100
4.6143-5.80950.22071440.18692478X-RAY DIFFRACTION100
5.8095-35.74570.26391540.2222572X-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)
12.0736-0.3578-0.15051.62540.271.6638-0.1829-0.1517-0.24530.04530.08490.37860.4039-0.3810.14970.3652-0.0650.02470.33290.00180.327916.7178-31.3977-43.2393
20.66220.5268-0.51112.1411-0.3591.4305-0.149-0.0066-0.0755-0.1530.06550.07530.198-0.05540.00310.20540.0225-0.00980.2626-0.02460.198519.591-19.8237-42.184
32.5831-0.69640.83950.68070.82552.4086-0.10450.24960.2741-0.16310.03920.2825-0.4557-0.73260.12920.35020.0707-0.06680.2808-0.03250.378211.3505-1.4853-48.0844
40.94530.5101-0.48311.4574-0.5831.1717-0.09920.040.0984-0.1041-0.00250.1585-0.0682-0.19110.12220.2650.0639-0.05490.269-0.05870.244619.9552-5.7486-43.1139
53.02670.9334-0.15452.8920.36563.55630.07930.10710.2310.0346-0.2229-0.0622-0.3477-0.07520.1570.23090.0224-0.0150.19160.01910.164241.1146-1.0672-28.9899
62.68971.63131.86141.58771.80942.5240.14930.0160.09330.1395-0.083-0.0750.24090.07560.00860.28430.02120.02280.24010.03970.286149.1918-1.3351-15.1442
73.16511.3042-1.42813.7244-0.93013.95870.1668-0.0232-0.0167-0.13620.1549-0.0106-0.06330.3121-0.25920.2801-0.0384-0.06770.19940.01270.479666.34048.0321-4.1062
83.7088-0.12722.81142.62750.00443.8191-0.3138-0.5799-0.08370.47820.07920.4453-0.2164-0.81070.11150.3164-0.06220.06390.5005-0.00010.238234.0706-12.6561-4.8497
91.4130.5969-1.5083.0426-1.02252.8335-0.111-0.3744-0.1817-0.1564-0.2578-0.248-0.01840.21640.20920.3025-0.045-0.01080.24980.01220.140741.5748-13.4887-15.1101
107.41110.4320.28071.3941-1.33243.4768-0.039-0.0111-0.8746-0.3796-0.1514-0.11050.92860.28660.29390.412-0.02560.04970.1392-0.00230.265940.9014-23.4062-14.2102
111.6901-0.07581.45881.95990.39732.05950.099-0.1423-0.25870.2870.10550.05150.4447-0.4313-0.22780.3091-0.09430.05470.310.00620.212738.8714-16.7659-7.8904
120.55861.0878-0.14032.18620.05670.6501-0.1045-0.59850.03770.3933-0.1203-0.1234-0.1637-0.69760.33960.16660.05930.0560.2656-0.0140.23242.9255-6.8247-2.2983
131.9454-0.3854-0.7621.68141.23762.26220.327-0.10810.4917-0.0187-0.0378-0.302-0.3742-0.027-0.2870.27740.0199-0.03570.2929-0.00530.528554.814911.85666.5429
141.2677-1.2424-0.06932.2462-0.59250.69050.2802-0.4085-0.0695-0.5772-0.09680.5042-0.15970.2461-0.13530.2946-0.0379-0.01720.43070.12530.518448.684410.55851.8571
152.40450.63620.9958.4928-0.32325.99120.3087-0.2701-0.30550.2305-0.1243-0.86131.14370.4587-0.45770.3197-0.0202-0.22440.2546-0.00940.184855.8997-5.61723.1908
163.75220.77340.08597.00441.48961.76470.1976-0.01580.75460.4227-0.1291-0.1606-0.3194-0.1207-0.12520.28190.03790.00210.3007-0.03570.450152.480315.695110.8753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 44 through 98 )
2X-RAY DIFFRACTION2chain 'G' and (resid 99 through 291 )
3X-RAY DIFFRACTION3chain 'G' and (resid 292 through 352 )
4X-RAY DIFFRACTION4chain 'G' and (resid 353 through 491 )
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 84 )
6X-RAY DIFFRACTION6chain 'H' and (resid 85 through 140 )
7X-RAY DIFFRACTION7chain 'H' and (resid 141 through 214 )
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 30 )
9X-RAY DIFFRACTION9chain 'L' and (resid 31 through 49 )
10X-RAY DIFFRACTION10chain 'L' and (resid 50 through 62 )
11X-RAY DIFFRACTION11chain 'L' and (resid 63 through 91 )
12X-RAY DIFFRACTION12chain 'L' and (resid 92 through 115 )
13X-RAY DIFFRACTION13chain 'L' and (resid 116 through 152 )
14X-RAY DIFFRACTION14chain 'L' and (resid 153 through 165 )
15X-RAY DIFFRACTION15chain 'L' and (resid 166 through 176 )
16X-RAY DIFFRACTION16chain 'L' and (resid 177 through 211 )

+
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