BMRB Entry 18218

Name: Backbone structure of human membrane protein HIGD1B
Published: 2012-05-22

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PDB ID: 2lon
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18218
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Backbone structure of human membrane protein HIGD1B

Deposition date:

2012-01-26

Original release date:

2012-05-22

Authors:

Klammt, Christian; Maslennikov, Innokentiy; Kwiatkowski, Witek; Choe, Senyon

Citation:

Citation: Klammt, Christian; Maslennikov, Innokentiy; Bayrhuber, Monika; Eichmann, Cedric; Vajpai, Navratna; Chiu, Ellis Jeremy Chua; Blain, Katherine; Esquivies, Luis; Kwon, June Hyun Jung; Balana, Bartosz; Pieper, Ursula; Sali, Andrej; Slesinger, Paul; Kwiatkowski, Witek; Riek, Roland; Choe, Senyon. "Facile backbone structure determination of human membrane proteins by NMR spectroscopy." Nat. Methods 9, 834-839 (2012).
PubMed: 22609626

Assembly members:

Assembly members:
entity, polymer, 99 residues, 11075.031 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: cell free synthesis Host organism: E. coli - cell free Vector: p23-GWN

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: MSANRRWWVPPDDEDCVSEK LLRKTRESPLVPIGLGGCLV VAAYRIYRLRSRGSTKMSIH LIHTRVAAQACAVGAIMLGA VYTMYSDYVKRMAQDAGEK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	356
15N chemical shifts	94
1H chemical shifts	558

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HIGD1B	1

Entities:

Entity 1, HIGD1B 99 residues - 11075.031 Da.

1

MET

SER

ALA

ASN

ARG

TRP

VAL

PRO

2

PRO

ASP

GLU

ASP

CYS

VAL

SER

GLU

LYS

3

LEU

ARG

LYS

THR

ARG

GLU

SER

PRO

LEU

4

VAL

PRO

ILE

GLY

LEU

GLY

CYS

LEU

VAL

5

VAL

ALA

TYR

ARG

ILE

TYR

ARG

LEU

ARG

6

SER

ARG

GLY

SER

THR

LYS

MET

SER

ILE

HIS

7

LEU

ILE

HIS

THR

ARG

VAL

ALA

GLN

ALA

8

CYS

ALA

VAL

GLY

ALA

ILE

MET

LEU

GLY

ALA

9

VAL

TYR

THR

MET

TYR

SER

ASP

TYR

VAL

LYS

10

ARG

MET

ALA

GLN

ASP

ALA

GLY

GLU

LYS

Samples:

samples_CDL: HIGD1B, [U-15N; U13C1], 0.2 mM; MES-Bis-TRIS 20 mM; LMPG 2%; DSS 0.5 mM; H2O 95%; D2O 5%

sample_N: HIGD1B, [U-15N], 0.2 mM; MES-Bis-TRIS 20 mM; LMPG 2%; DSS 0.5 mM; H2O 95%; D2O 5%

sample_CN: HIGD1B, [U-15N; U-13C], 0.2 mM; MES-Bis-TRIS 20 mM; LMPG 2%; DSS 0.5 mM; H2O 95%; D2O 5%

sample_CND: HIGD1B, [U-15N; U-13C; U-2H], 0.2 mM; MES-Bis-TRIS 20 mM; LMPG 2%; DSS 0.5 mM; H2O 95%; D2O 5%

sample_CN-dLMPG: HIGD1B, [U-15N; U-13C], ?0.2 mM; MES-Bis-TRIS 20 mM; d27-LMPG, 95%-2H in alkyl chain, 2%; DSS 0.5 mM; H2O 95%; D2O 5%

samples_SL: HIGD1B, [U-15N], 0.2 mM; MES-Bis-TRIS 20 mM; LMPG 2%; DSS 0.5 mM; H2O 95%; D2O 5%

samples_DL: HIGD1B, [U-15N], 0.2 mM; MES-Bis-TRIS 20 mM; LMPG 2%; DSS 0.5 mM; H2O 95%; D2O 5%

sample_ND: HIGD1B, [U-15N; U-2H], 0.2 mM; MES-Bis-TRIS 20 mM; LMPG 2%; DSS 0.5 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 40 mM; pH: 6.0; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_N	isotropic	sample_conditions_1
2D 1H-15N HSQC	samples_CDL	isotropic	sample_conditions_1
2D HNCO	samples_CDL	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_CN	isotropic	sample_conditions_1
3D HNCO	sample_CND	isotropic	sample_conditions_1
3D HNHA	sample_CND	isotropic	sample_conditions_1
3D HNCACB	sample_CND	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_N	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_CN-dLMPG	isotropic	sample_conditions_1
3D 13C-15N HSQC-NOESY-HSQC	sample_CN	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_ND	isotropic	sample_conditions_1
2D 1H-15N HSQC	samples_SL	isotropic	sample_conditions_1
2D 1H-15N HSQC	samples_DL	isotropic	sample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

CARA, Keller and Wuthrich - chemical shift assignment, data analysis

PROSA, Guntert - processing

MCCL, (MCCL) Kwiatkowski, Maslennikov - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

Molmol, Koradi, Billeter and Wuthrich - structure analysis, structure visualization

NMR spectrometers:

Bruker DRX 700 MHz
Varian Uniform NMR System 500 MHz

PDB	2LON
DBJ	BAA90725 BAA90726
GB	AAH20667 EAW51575 EAW51576
REF	NP_001258809 NP_057522 XP_001146933 XP_002827469 XP_002827470
SP	Q9P298
AlphaFold	Q9P298